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7. Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike

Author

Wang, Qian, Guo, Yicheng, Liu, Liyuan, Schwanz, Logan T., Li, Zhiteng, Nair, Manoj S., Ho, Jerren, Zhang, Richard M., Iketani, Sho, Yu, Jian, Huang, Yiming, Qu, Yiming, Valdez, Riccardo, Lauring, Adam S., Huang, Yaoxing, Gordon, Aubree, Wang, Harris H., Liu, Lihong, and Ho, David D.

Published
2023
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8. SARS-CoV-2 omicron BA.2.87.1 exhibits higher susceptibility to serum neutralization than EG.5.1 and JN.1

Author

Qian Wang, Yicheng Guo, Logan T. Schwanz, Ian A. Mellis, Yiwei Sun, Yiming Qu, Guillaume Urtecho, Riccardo Valdez, Emily Stoneman, Aubree Gordon, Harris H. Wang, David D. Ho, and Lihong Liu

Subjects
COVID-19, SARS-CoV-2, EG.5.1, JN.1, BA.2.87.1, polyclonal sera, mRNA vaccines, Infectious and parasitic diseases, RC109-216, Microbiology, QR1-502
Abstract

As SARS-CoV-2 continues to spread and mutate, tracking the viral evolutionary trajectory and understanding the functional consequences of its mutations remain crucial. Here, we characterized the antibody evasion, ACE2 receptor engagement, and viral infectivity of the highly mutated SARS-CoV-2 Omicron subvariant BA.2.87.1. Compared with other Omicron subvariants, including EG.5.1 and the current predominant JN.1, BA.2.87.1 exhibits less immune evasion, reduced viral receptor engagement, and comparable infectivity in Calu-3 lung cells. Intriguingly, two large deletions (Δ15-26 and Δ136-146) in the N-terminal domain (NTD) of the spike protein facilitate subtly increased antibody evasion but significantly diminish viral infectivity. Collectively, our data support the announcement by the USA CDC that the public health risk posed by BA.2.87.1 appears to be low.

Published
2024
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17. COVID-19 vaccines and adverse events of special interest: A multinational Global Vaccine Data Network (GVDN) cohort study of 99 million vaccinated individuals

Author

Faksova, K., Walsh, D., Jiang, Y., Griffin, J., Phillips, A., Gentile, A., Kwong, J.C., Macartney, K., Naus, M., Grange, Z., Escolano, S., Sepulveda, G., Shetty, A., Pillsbury, A., Sullivan, C., Naveed, Z., Janjua, N.Z., Giglio, N., Perälä, J., Nasreen, S., Gidding, H., Hovi, P., Vo, T., Cui, F., Deng, L., Cullen, L., Artama, M., Lu, H., Clothier, H.J., Batty, K., Paynter, J., Petousis-Harris, H., Buttery, J., Black, S., and Hviid, A.

Published
2024
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18. Constraints on Lightly Ionizing Particles from CDMSlite

Author

SuperCDMS Collaboration, Alkhatib, I., Amaral, D. W. P., Aralis, T., Aramaki, T., Arnquist, I. J., Langroudy, I. Ataee, Azadbakht, E., Banik, S., Barker, D., Bathurst, C., Bauer, D. A., Bezerra, L. V. S., Bhattacharyya, R., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Calkins, R., Cameron, R. A., Cartaro, C., Cerdeño, D. G., Chang, Y. -Y., Chaudhuri, M., Chen, R., Chott, N., Cooley, J., Coombes, H., Corbett, J., Cushman, P., De Brienne, F., di Vacri, M. L., Diamond, M. D., Fascione, E., Figueroa-Feliciano, E., Fink, C. W., Fouts, K., Fritts, M., Gerbier, G., Germond, R., Ghaith, M., Golwala, S. R., Harris, H. R., Hines, B. A., Hollister, M. I., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Kashyap, V. K. S., Kelsey, M. H., Kubik, A., Kurinsky, N. A., Lawrence, R. E., Li, A., Loer, B., Asamar, E. Lopez, Lukens, P., MacFarlane, D. B., Mahapatra, R., Mandic, V., Mast, N., Mayer, A. J., Theenhausen, H. Meyer zu, Michaud, É. M., Michielin, E., Mirabolfathi, N., Mohanty, B., Mendoza, J. D. Morales, Nagorny, S., Nelson, J., Neog, H., Novati, V., Orrell, J. L., Oser, S. M., Page, W. A., Partridge, R., Podviianiuk, R., Ponce, F., Poudel, S., Pradeep, A., Pyle, M., Rau, W., Reid, E., Ren, R., Reynolds, T., Roberts, A., Robinson, A. E., Saab, T., Sadoulet, B., Sander, J., Sattari, A., Schnee, R. W., Scorza, S., Serfass, B., Sincavage, D. J., Stanford, C., Street, J., Toback, D., Underwood, R., Verma, S., Villano, A. N., von Krosigk, B., Watkins, S. L., Wilson, J. S., Wilson, M. J., Winchell, J., Wright, D. H., Yellin, S., Young, B. A., Yu, T. C., Zhang, E., Zhang, H. G., Zhao, X., and Zheng, L.

Subjects
High Energy Physics - Experiment, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - High Energy Astrophysical Phenomena, High Energy Physics - Phenomenology, Physics - Instrumentation and Detectors
Abstract

The Cryogenic Dark Matter Search low ionization threshold experiment (CDMSlite) achieved efficient detection of very small recoil energies in its germanium target, resulting in sensitivity to Lightly Ionizing Particles (LIPs) in a previously unexplored region of charge, mass, and velocity parameter space. We report first direct-detection limits calculated using the optimum interval method on the vertical intensity of cosmogenically-produced LIPs with an electric charge smaller than $e/(3\times10^5$), as well as the strongest limits for charge $\leq e/160$, with a minimum vertical intensity of $1.36\times10^{-7}$\,cm$^{-2}$s$^{-1}$sr$^{-1}$ at charge $e/160$. These results apply over a wide range of LIP masses (5\,MeV/$c^2$ to 100\,TeV/$c^2$) and cover a wide range of $\beta\gamma$ values (0.1 -- $10^6$), thus excluding non-relativistic LIPs with $\beta\gamma$ as small as 0.1 for the first time.

Published
2020
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19. Light Dark Matter Search with a High-Resolution Athermal Phonon Detector Operated Above Ground

Author

Alkhatib, I., Amaral, D. W. P., Aralis, T., Aramaki, T., Arnquist, I. J., Langroudy, I. Ataee, Azadbakht, E., Banik, S., Barker, D., Bathurst, C., Bauer, D. A., Bezerra, L. V. S., Bhattacharyya, R., Binder, T., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Calkins, R., Cameron, R. A., Cartaro, C., Cerdeño, D. G., Chang, Y. -Y., Chaudhuri, M., Chen, R., Chott, N., Cooley, J., Coombes, H., Corbett, J., Cushman, P., De Brienne, F., di Vacri, M. L., Diamond, M. D., Fascione, E., Figueroa-Feliciano, E., Fink, C. W., Fouts, K., Fritts, M., Gerbier, G., Germond, R., Ghaith, M., Golwala, S. R., Harris, H. R., Herbert, N., Hines, B. A., Hollister, M. I., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Kashyap, V. K. S., Kelsey, M. H., Kubik, A., Kurinsky, N. A., Lawrence, R. E., Li, A., Loer, B., Asamar, E. Lopez, Lukens, P., MacDonell, D., MacFarlane, D. B., Mahapatra, R., Mandic, V., Mast, N., Mayer, A. J., Theenhausen, H. Meyer zu, Michaud, É. M., Michielin, E., Mirabolfathi, N., Mohanty, B., Mendoza, J. D. Morales, Nagorny, S., Nelson, J., Neog, H., Novati, V., Orrell, J. L., Oser, S. M., Page, W. A., Pakarha, P., Partridge, R., Podviianiuk, R., Ponce, F., Poudel, S., Pyle, M., Rau, W., Reid, E., Ren, R., Reynolds, T., Roberts, A., Robinson, A. E., Saab, T., Sadoulet, B., Sander, J., Sattari, A., Schnee, R. W., Scorza, S., Serfass, B., Sincavage, D. J., Stanford, C., Street, J., Toback, D., Underwood, R., Verma, S., Villano, A. N., von Krosigk, B., Watkins, S. L., Wills, L., Wilson, J. S., Wilson, M. J., Winchell, J., Wright, D. H., Yellin, S., Young, B. A., Yu, T. C., Zhang, E., Zhang, H. G., Zhao, X., Zheng, L., Camilleri, J., Kolomensky, Yu. G., and Zuber, S.

Subjects
High Energy Physics - Experiment, Astrophysics - Cosmology and Nongalactic Astrophysics, Physics - Instrumentation and Detectors
Abstract

We present limits on spin-independent dark matter-nucleon interactions using a $10.6$ $\mathrm{g}$ Si athermal phonon detector with a baseline energy resolution of $\sigma_E=3.86 \pm 0.04$ $(\mathrm{stat.})^{+0.19}_{-0.00}$ $(\mathrm{syst.})$ $\mathrm{eV}$. This exclusion analysis sets the most stringent dark matter-nucleon scattering cross-section limits achieved by a cryogenic detector for dark matter particle masses from $93$ to $140$ $\mathrm{MeV}/c^2$, with a raw exposure of $9.9$ $\mathrm{g}\cdot\mathrm{d}$ acquired at an above-ground facility. This work illustrates the scientific potential of detectors with athermal phonon sensors with eV-scale energy resolution for future dark matter searches., Comment: 7 pages, 4 figures, this version includes ancillary files from official data release

Published
2020
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20. Constraints on low-mass, relic dark matter candidates from a surface-operated SuperCDMS single-charge sensitive detector

Author

SuperCDMS Collaboration, Amaral, D. W., Aralis, T., Aramaki, T., Arnquist, I. J., Azadbakht, E., Banik, S., Barker, D., Bathurst, C., Bauer, D. A., Bezerra, L. V. S., Bhattacharyya, R., Binder, T., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Calkins, R., Cameron, R. A., Cartaro, C., Cerdeño, D. G., Chang, Y. -Y., Chen, R., Chott, N., Cooley, J., Coombes, H., Corbett, J., Cushman, P., De Brienne, F., di Vacri, M. L., Diamond, M. D., Fascione, E., Figueroa-Feliciano, E., Fink, C. W., Fouts, K., Fritts, M., Gerbier, G., Germond, R., Ghaith, M., Golwala, S. R., Harris, H. R., Herbert, N., Hines, B. A., Hollister, M. I., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Kelsey, M. H., Kubik, A., Kurinsky, N. A., Lawrence, R. E., Li, A., Loer, B., Asamar, E. Lopez, Lukens, P., MacDonell, D., MacFarlane, D. B., Mahapatra, R., Mandic, V., Mast, N., Mayer, A. J., Michaud, É. M., Michielin, E., Mirabolfathi, N., Mohanty, B., Mendoza, J. D. Morales, Nagorny, S., Nelson, J., Neog, H., Novati, V., Orrell, J. L., Oser, S. M., Page, W. A., Pakarha, P., Partridge, R., Podviianiuk, R., Ponce, F., Poudel, S., Pyle, M., Rau, W., Reid, E., Ren, R., Reynolds, T., Roberts, A., Robinson, A. E., Rogers, H. E., Saab, T., Sadoulet, B., Sander, J., Sattari, A., Schnee, R. W., Scorza, S., Serfass, B., Sincavage, D. J., Stanford, C., Stein, M., Street, J., Toback, D., Underwood, R., Verma, S., Villano, A. N., von Krosigk, B., Watkins, S. L., Wills, L., Wilson, J. S., Wilson, M. J., Winchell, J., Wright, D. H., Yellin, S., Young, B. A., Yu, T. C., Zhang, E., Zhang, H. G., Zhao, X., and Zheng, L.

Subjects
High Energy Physics - Experiment, Astrophysics - Cosmology and Nongalactic Astrophysics, Physics - Instrumentation and Detectors
Abstract

This article presents an analysis and the resulting limits on light dark matter inelastically scattering off of electrons, and on dark photon and axion-like particle absorption, using a second-generation SuperCDMS high-voltage eV-resolution detector. The 0.93 gram Si detector achieved a 3 eV phonon energy resolution; for a detector bias of 100 V, this corresponds to a charge resolution of 3% of a single electron-hole pair. The energy spectrum is reported from a blind analysis with 1.2 gram-days of exposure acquired in an above-ground laboratory. With charge carrier trapping and impact ionization effects incorporated into the dark matter signal models, the dark matter-electron cross section $\bar{\sigma}_{e}$ is constrained for dark matter masses from 0.5--$10^{4} $MeV$/c^{2}$; in the mass range from 1.2--50 eV$/c^{2}$ the dark photon kinetic mixing parameter $\varepsilon$ and the axioelectric coupling constant $g_{ae}$ are constrained. The minimum 90% confidence-level upper limits within the above mentioned mass ranges are $\bar{\sigma}_{e}\,=\,8.7\times10^{-34}$ cm$^{2}$, $\varepsilon\,=\,3.3\times10^{-14}$, and $g_{ae}\,=\,1.0\times10^{-9}$., Comment: 5 pages + title and references, 3 figures and 1 table

Published
2020
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22. Constraints on dark photons and axion-like particles from SuperCDMS Soudan

Author

SuperCDMS Collaboration, Aralis, T., Aramaki, T., Arnquist, I. J., Azadbakht, E., Baker, W., Banik, S., Barker, D., Bathurst, C., Bauer, D. A., Bezerra, L. V. S, Bhattacharyya, R., Binder, T., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Calkins, R., Cameron, R. A., Cartaro, C., Cerdeño, D. G., Chang, Y. -Y., Cooley, J., Coombes, H., Corbett, J., Cornell, B., Cushman, P., De Brienne, F., di Vacri, M. L., Diamond, M. D., Fascione, E., Figueroa-Feliciano, E., Fink, C. W., Fouts, K., Fritts, M., Gerbier, G., Germond, R., Ghaith, M., Golwala, S. R., Harris, H. R., Herbert, N., Hines, B. A., Hollister, M. I., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Kelsey, M. H., Kennedy, A., Kubik, A., Kurinsky, N. A., Lawrence, R. E., Li, A., Loer, B., Asamar, E. Lopez, Lukens, P., MacDonell, D., MacFarlane, D. B., Mahapatra, R., Mandic, V., Mast, N., Michaud, É. M., Michielin, E., Mirabolfathi, N., Mohanty, B., Mendoza, J. D. Morales, Nagorny, S., Nelson, J., Neog, H., Orrell, J. L., Oser, S. M., Page, W. A., Pakarha, P., Partridge, R., Podviianiuk, R., Ponce, F., Poudel, S., Pyle, M., Rau, W., Ren, R., Reynolds, T., Roberts, A., Robinson, A. E., Rogers, H. E., Saab, T., Sadoulet, B., Sander, J., Toback, D., Underwood, R., Verma, S., Villano, A. N., von Krosigk, B., Watkins, S. L., Wills, L., Wilson, J. S., Wilson, M. J., Winchell, J., Wright, D. H., Yellin, S., Young, B. A., Yu, T. C., Zhang, E., Zhao, X., and Zheng, L.

Subjects
High Energy Physics - Experiment, Physics - Instrumentation and Detectors
Abstract

We present an analysis of electron recoils in cryogenic germanium detectors operated during the SuperCDMS Soudan experiment. The data are used to set new constraints on the axioelectric coupling of axion-like particles and the kinetic mixing parameter of dark photons, assuming the respective species constitutes all of the galactic dark matter. This study covers the mass range from 40 eV/$c^2$ to 500 eV/$c^2$ for both candidates, excluding previously untested parameter space for masses below ~1 keV/$c^2$. For the kinetic mixing of dark photons, values below $10^{-15}$ are reached for particle masses around 100 eV/$c^2$; for the axioelectric coupling of axion-like particles, values below $10^{-12}$ are reached for particles with masses in the range of a few-hundred eV/$c^2$., Comment: 14 pages, 10 figures, 1 page correction included with 3 figures

Published
2019
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23. Factors Associated With Large Improvements in Health-Related Quality of Life in Patients With Atrial Fibrillation

Author

Steinberg, Benjamin A, Holmes, DaJuanicia N, Pieper, Karen, Allen, Larry A, Chan, Paul S, Ezekowitz, Michael D, Freeman, James V, Fonarow, Gregg C, Gersh, Bernard J, Hylek, Elaine M, Kowey, Peter R, Mahaffey, Kenneth W, Naccarelli, Gerald, Reiffel, James, Singer, Daniel E, Peterson, Eric D, Piccini, Jonathan P, Mendelson, R, Nahhas, A, Neutel, J, Padanilam, B, Pan, D, Poock, J, Raffetto, J, Greengold, R, Roan, P, Saba, F, Sackett, M, Schneider, R, Seymour, Z, Shanes, J, Shoemaker, J, Simms, V, Smiley, N, Smith, D, Snipes, C, Sotolongo, R, Staniloae, C, Stoltz, S, Suresh, DP, Tak, T, Tannenbaum, A, Turk, S, Vora, K, Randhawa, P, Zebrack, J, Silva, E, Riley, E, Weinstein, D, Vasiliauskas, T, Goldbarg, S, Hayward, D, Yarlagadda, C, Laurion, D, Osunkoya, A, Burns, R, Castor, T, Spiller, D, Luttman, C, Anton, S, McGarvey, J, Guthrie, R, Deriso, G, Flood, R, Fleischer, L, Fierstein, JS, Aggarwal, R, Jacobs, G, Adjei, N, Akyea-Djamson, A, Alfieri, A, Bacon, J, Bedwell, N, Berger, P, Berry, J, Bhagwat, R, Bloom, S, Boccalandro, F, Capo, J, Kapadia, S, Casanova, R, Morriss III, JE, Christensen, T, Elsen, J, Farsad, R, Fox, D, Frandsen, B, Gelernt, M, Gill, S, Grubb, S, Hall, C, Harris, H, Hotchkiss, D, Ip, J, Jaffrani, N, Jones, A, Kazmierski, J, Waxman, F, Kneller, GL, and Labroo, A

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Heart Disease, Substance Misuse, Genetics, Health Services, Cardiovascular, Clinical Research, Good Health and Well Being, Aged, Aged, 80 and over, Anti-Arrhythmia Agents, Atrial Fibrillation, Catheter Ablation, Comorbidity, Electric Countershock, Female, Health Status, Heart Rate, Humans, Male, Outpatients, Quality of Life, Recovery of Function, Registries, Risk Factors, Time Factors, Treatment Outcome, United States, ORBIT-AF (Outcomes Registry for Better Informed Treatment of Atrial Fibrillation) Investigators and Patients, atrial fibrillation, cardiac resynchronization therapy, health status, patient-reported outcomes, quality of life, Cardiorespiratory Medicine and Haematology, Medical Physiology, Cardiovascular System & Hematology, Cardiovascular medicine and haematology, Clinical sciences, Medical physiology
Abstract

BackgroundAtrial fibrillation (AF) adversely impacts health-related quality of life (hrQoL). While some patients demonstrate improvements in hrQoL, the factors associated with large improvements in hrQoL are not well described.MethodsWe assessed factors associated with a 1-year increase in the Atrial Fibrillation Effect on Quality-of-Life score of 1 SD (≥18 points; 3× clinically important difference), among outpatients in the Outcomes Registry for Better Informed Treatment of Atrial Fibrillation I registry.ResultsOverall, 28% (181/636) of patients had such a hrQoL improvement. Compared with patients not showing large hrQoL improvement, they were of similar age (median 73 versus 74, P=0.3), equally likely to be female (44% versus 48%, P=0.3), but more likely to have newly diagnosed AF at baseline (18% versus 8%; P=0.0004), prior antiarrhythmic drug use (52% versus 40%, P=0.005), baseline antiarrhythmic drug use (34.8% versus 26.8%, P=0.045), and more likely to undergo AF-related procedures during follow-up (AF ablation: 6.6% versus 2.0%, P=0.003; cardioversion: 12.2% versus 5.9%, P=0.008). In multivariable analysis, a history of alcohol abuse (adjusted OR, 2.41; P=0.01) and increased baseline diastolic blood pressure (adjusted OR, 1.23 per 10-point increase and >65 mm Hg; P=0.04) were associated with large improvements in hrQoL at 1 year, whereas patients with prior stroke/transient ischemic attack, chronic obstructive pulmonary disease, and peripheral arterial disease were less likely to improve (P

Published
2020

24. 2017 NIH-wide workshop report on “The Human Microbiome: Emerging Themes at the Horizon of the 21st Century”

Author

Alm, Eric, Borenstein, Elhanan, Britton, Robert A, Bultman, Scott J, Chang, Eugene B, Cho, Mildred, Dantas, Gautam, Dominguez-Bello, Maria Gloria, Donovan, Sharon M, Dorrestein, Pieter, Douglas, Angela E, Gewirtz, Andrew, Ghannoum, Mahmoud, Goodman, Andrew L, Gordon, Jeffrey I, Huffnagle, Gary B, Jenq, Robert R, Jia, Wei, Knight, Rob, Koropatkin, Nicole, Lampe, Johanna W, Lu, Timothy, Ochman, Howard, Pamer, Eric G, Patterson, Andrew D, Philpott, Dana, Pollard, Katherine S, Rawls, John F, Salzman, Nita H, Sears, Cynthia L, Stappenbeck, Thaddeus, Taga, Michiko E, Turnbaugh, Peter J, Wang, Harris H, Wu, Gary D, and Xavier, Ramnik J

Subjects
Biological Sciences, Genetics, Good Health and Well Being, Humans, Internet, Microbiota, National Institutes of Health (U.S.), United States, Human microbiome, HMP, NIH, National Microbiome Initiative, NIH-wide microbiome workshop writing team, Ecology, Microbiology, Medical Microbiology, Evolutionary biology
Abstract

The National Institutes of Health (NIH) organized a three-day human microbiome research workshop, August 16-18, 2017, to highlight the accomplishments of the 10-year Human Microbiome Project program, the outcomes of the investments made by the 21 NIH Institutes and Centers which now fund this area, and the technical challenges and knowledge gaps which will need to be addressed in order for this field to advance over the next 10 years. This report summarizes the key points in the talks, round table discussions, and Joint Agency Panel from this workshop.

Published
2019

26. Background rates of adverse events of special interest for COVID-19 vaccines: A multinational Global Vaccine Data Network (GVDN) analysis

Author

Phillips, A., Jiang, Y., Walsh, D., Andrews, N., Artama, M., Clothier, H., Cullen, L., Deng, L., Escolano, S., Gentile, A., Gidding, G., Giglio, N., Junker, T., Huang, W., Janjua, N., Kwong, J., Li, J., Nasreen, S., Naus, M., Naveed, Z., Pillsbury, A., Stowe, J., Vo, T., Buttery, J., Petousis-Harris, H., Black, S., and Hviid, A.

Published
2023
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28. Search for Low-Mass Dark Matter with CDMSlite Using a Profile Likelihood Fit

Author

SuperCDMS Collaboration, Agnese, R., Aralis, T., Aramaki, T., Arnquist, I. J., Azadbakht, E., Baker, W., Banik, S., Barker, D., Bauer, D. A., Binder, T., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Calkins, R., Cameron, R. A., Cartaro, C., Cerdeño, D. G., Chang, Y. -Y., Cooley, J., Cornell, B., Cushman, P., De Brienne, F., Doughty, T., Fascione, E., Figueroa-Feliciano, E., Fink, C. W., Fritts, M., Gerbier, G., Germond, R., Ghaith, M., Golwala, S. R., Harris, H. R., Herbert, N., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Jena, C., Kelsey, M. H., Kennedy, A., Kubik, A., Kurinsky, N. A., Lawrence, R. E., Loer, B., Asamar, E. Lopez, Lukens, P., MacDonell, D., Mahapatra, R., Mandic, V., Mast, N., Miller, E., Mirabolfathi, N., Mohanty, B., Mendoza, J. D. Morales, Nelson, J., Neog, H., Orrell, J. L., Oser, S. M., Page, W. A., Partridge, R., Pepin, M., Ponce, F., Poudel, S., Pyle, M., Qiu, H., Rau, W., Reisetter, A., Ren, R., Reynolds, T., Roberts, A., Robinson, A. E., Rogers, H. E., Saab, T., Sadoulet, B., Sander, J., Scarff, A., Schnee, R. W., Scorza, S., Senapati, K., Serfass, B., Speller, D., Stanford, C., Stein, M., Street, J., Tanaka, H. A., Toback, D., Underwood, R., Villano, A. N., von Krosigk, B., Watkins, S. L., Wilson, J. S., Wilson, M. J., Winchell, J., Wright, D. H., Yellin, S., Young, B. A., Zhang, X., and Zhao, X.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Physics - Instrumentation and Detectors
Abstract

The Cryogenic Dark Matter Search low ionization threshold experiment (CDMSlite) searches for interactions between dark matter particles and germanium nuclei in cryogenic detectors. The experiment has achieved a low energy threshold with improved sensitivity to low-mass (<10 GeV/c$^2$) dark matter particles. We present an analysis of the final CDMSlite data set, taken with a different detector than was used for the two previous CDMSlite data sets. This analysis includes a data "salting" method to protect against bias, improved noise discrimination, background modeling, and the use of profile likelihood methods to search for a dark matter signal in the presence of backgrounds. We achieve an energy threshold of 70 eV and significantly improve the sensitivity for dark matter particles with masses between 2.5 and 10 GeV/c$^2$ compared to previous analyses. We set an upper limit on the dark matter-nucleon scattering cross section in germanium of 5.4$\times$10$^{-42}$ cm$^2$ at 5 GeV/c$^2$, a factor of $\sim$2.5 improvement over the previous CDMSlite result.

Published
2018
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29. Production Rate Measurement of Tritium and Other Cosmogenic Isotopes in Germanium with CDMSlite

Author

SuperCDMS Collaboration, Agnese, R., Aralis, T., Aramaki, T., Arnquist, I. J., Azadbakht, E., Baker, W., Barker, D., Bauer, D. A., Binder, T., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Calkins, R., Cartaro, C., Cerdeño, D. G., Chang, Y. -Y., Cooley, J., Cornell, B., Cushman, P., Doughty, T., Fascione, E., Figueroa-Feliciano, E., Fink, C. W., Fritts, M., Gerbier, G., Germond, R., Ghaith, M., Golwal, S. R., Harris, H. R., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Jena, C., Kelsey, M. H., Kennedy, A., Kubik, A., Kurinsky, N. A., Lawrence, R. E., Loer, B., Asamar, E. Lopez, Lukens, P., MacDonell, D., Mahapatra, R., Mandic, V., Mast, N., Miller, E., Mirabolfathi, N., Mohanty, B., Mendoza, J. D. Morales, Nelson, J., Orrell, J. L., Oser, S. M., Page, W. A., Partridge, R., Pepin, M., Ponce, F., Poudel, S., Pyle, M., Qiu, H., Rau, W., Reisetter, A., Ren, R., Reynolds, T., Roberts, A., Robinson, A. E., Rogers, H. E., Saab, T., Sadoulet, B., Banik, S., Sander, J., Scarff, A., Schnee, R. W., Scorza, S., Senapati, K., Serfass, B., Speller, D., Stein, M., Street, J., Tanaka, H. A., Toback, D., Underwood, R., Villano, A. N., von Krosigk, B., Watkins, S. L., Wilson, J. S., Wilson, M. J., Winchell, J., Wright, D. H., Yellin, S., Young, B. A., Zhang, X., and Zhao, X.

Subjects
Physics - Instrumentation and Detectors, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment, Nuclear Experiment
Abstract

Future direct searches for low-mass dark matter particles with germanium detectors, such as SuperCDMS SNOLAB, are expected to be limited by backgrounds from radioactive isotopes activated by cosmogenic radiation inside the germanium. There are limited experimental data available to constrain production rates and a large spread of theoretical predictions. We examine the calculation of expected production rates, and analyze data from the second run of the CDMS low ionization threshold experiment (CDMSlite) to estimate the rates for several isotopes. We model the measured CDMSlite spectrum and fit for contributions from tritium and other isotopes. Using the knowledge of the detector history, these results are converted to cosmogenic production rates at sea level. The production rates in atoms/(kg$\cdot$day) are 74$\pm$9 for $^3$H, 1.5$\pm$0.7 for $^{55}$Fe, 17$\pm$5 for $^{65}$Zn, and 30$\pm$18 for $^{68}$Ge., Comment: 14 pages, 10 figures, 5 tables. v5 contains the extended data release (and documentation) of the CDMSlite Run 2 data as ancillary files

Published
2018
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30. First Dark Matter Constraints from a SuperCDMS Single-Charge Sensitive Detector

Author

SuperCDMS Collaboration, Agnese, R., Aralis, T., Aramaki, T., Arnquist, I. J., Azadbakht, E., Baker, W., Banik, S., Barker, D., Bauer, D. A., Binder, T., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Calkins, R., Cartaro, C., Cerdeno, D. G., Chang, Y. -Y., Cooley, J., Cornell, B., Cushman, P., Di Stefano, P. C. F., Doughty, T., Fascione, E., Figueroa-Feliciano, E., Fink, C., Fritts, M., Gerbier, G., Germond, R., Ghaith, M., Golwala, S. R., Harris, H. R., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jena, C., Kelsey, M. H., Kennedy, A., Kubik, A., Kurinsky, N. A., Lawrence, R. E., Leyva, J. V., Loer, B., Asamar, E. Lopez, Lukens, P., MacDonell, D., Mahapatra, R., Mandic, V., Mast, N., Miller, E. H., Mirabolfathi, N., Mohanty, B., Mendoza, J. D. Morales, Nelson, J., Orrell, J. L., Oser, S. M., Page, W. A., Partridge, R., Pepin, M., Phipps, A., Ponce, F., Poudel, S., Pyle, M., Qiu, H., Rau, W., Reisetter, A., Reynolds, T., Roberts, A., Robinson, A. E., Rogers, H. E., Romani, R. K., Saab, T., Sadoulet, B., Sander, J., Scarff, A., Schnee, R. W., Scorza, S., Senapati, K., Serfass, B., So, J., Speller, D., Stanford, C., Stein, M., Street, J., Tanaka, H. A., Toback, D., Underwood, R., Villano, A. N., von Krosigk, B., Watkins, S. L., Wilson, J. S., Wilson, M. J., Winchell, J., Wright, D. H., Yellin, S., Young, B. A., Zhang, X., and Zhao, X.

Subjects
High Energy Physics - Experiment, Astrophysics - Cosmology and Nongalactic Astrophysics, Physics - Instrumentation and Detectors
Abstract

We present the first limits on inelastic electron-scattering dark matter and dark photon absorption using a prototype SuperCDMS detector having a charge resolution of 0.1 electron-hole pairs (CDMS HVeV, a 0.93 gram CDMS HV device). These electron-recoil limits significantly improve experimental constraints on dark matter particles with masses as low as 1 MeV/$\mathrm{c^2}$. We demonstrate a sensitivity to dark photons competitive with other leading approaches but using substantially less exposure (0.49 gram days). These results demonstrate the scientific potential of phonon-mediated semiconductor detectors that are sensitive to single electronic excitations., Comment: 6 pages + title and references, 6 figures, includes erratum submitted to PRL and data release

Published
2018
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31. Nuclear-recoil energy scale in CDMS II silicon dark-matter detectors

Author

Agnese, R., Anderson, A. J., Aramaki, T., Baker, W., Balakishiyeva, D., Banik, S., Barker, D., Thakur, R. Basu, Bauer, D. A., Binder, T., Borgland, A., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Caldwell, D. O., Calkins, R., Cartaro, C., Cerdeno, D. G., Chagani, H., Chang, Y. -Y., Chen, Y., Cooley, J., Cornell, B., Cushman, P., Daal, M., Doughty, T., Dragowsky, E. M., Esteban, L., Fallows, S., Fascione, E., Figueroa-Feliciano, E., Fritts, M., Gerbier, G., Germond, R., Ghaith, M., Godfrey, G. L., Golwala, S. R., Hall, J., Harris, H. R., Holmgren, D., Hong, Z., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Jena, C., Kelsey, M. H., Kennedy, A., Kubik, A., Kurinsky, N. A., Leder, A., Asamar, E. Lopez, Lukens, P., MacDonell, D., Mahapatra, R., Mandic, V., Mast, N., McCarthy, K. A., Miller, E. H., Mirabolfathi, N., Moffatt, R. A., Mohanty, B., Moore, D., Mendoza, J. D. Morales, Nelson, J., Oser, S. M., Page, K., Page, W. A., Partridge, R., Martinez, M. Penalver, Pepin, M., Phipps, A., Poudel, S., Pyle, M., Qiu, H., Rau, W., Redl, P., Reisetter, A., Roberts, A., Rogers, H. E., Robinson, A. E., Saab, T., Sadoulet, B., Sander, J., Schneck, K., Schnee, R. W., Scorza, S., Senapati, K., Serfass, B., Speller, D., Di Stefano, P. C. F., Stein, M., Street, J., Tanaka, H. A., Toback, D., Underwood, R., Villano, A. N., von Krosigk, B., Welliver, B., Wilson, J. S., Wilson, M. J., Wright, D. H., Yellin, S., Yen, J. J., Young, B. A., Zhang, X., and Zhao, X.

Subjects
Physics - Instrumentation and Detectors, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment
Abstract

The Cryogenic Dark Matter Search (CDMS II) experiment aims to detect dark matter particles that elastically scatter from nuclei in semiconductor detectors. The resulting nuclear-recoil energy depositions are detected by ionization and phonon sensors. Neutrons produce a similar spectrum of low-energy nuclear recoils in such detectors, while most other backgrounds produce electron recoils. The absolute energy scale for nuclear recoils is necessary to interpret results correctly. The energy scale can be determined in CDMS II silicon detectors using neutrons incident from a broad-spectrum $^{252}$Cf source, taking advantage of a prominent resonance in the neutron elastic scattering cross section of silicon at a recoil (neutron) energy near 20 (182) keV. Results indicate that the phonon collection efficiency for nuclear recoils is $4.8^{+0.7}_{-0.9}$% lower than for electron recoils of the same energy. Comparisons of the ionization signals for nuclear recoils to those measured previously by other groups at higher electric fields indicate that the ionization collection efficiency for CDMS II silicon detectors operated at $\sim$4 V/cm is consistent with 100% for nuclear recoils below 20 keV and gradually decreases for larger energies to $\sim$75% at 100 keV. The impact of these measurements on previously published CDMS II silicon results is small., Comment: 22 pages, 17 figures, 1 table, 1 appendix

Published
2018
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32. Antibody evasion properties of SARS-CoV-2 Omicron sublineages

Author

Iketani, Sho, Liu, Lihong, Guo, Yicheng, Liu, Liyuan, Chan, Jasper F.-W., Huang, Yiming, Wang, Maple, Luo, Yang, Yu, Jian, Chu, Hin, Chik, Kenn K.-H., Yuen, Terrence T.-T., Yin, Michael T., Sobieszczyk, Magdalena E., Huang, Yaoxing, Yuen, Kwok-Yung, Wang, Harris H., Sheng, Zizhang, and Ho, David D.

Published
2022
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34. Author Correction: Genome-wide association and epidemiological analyses reveal common genetic origins between uterine leiomyomata and endometriosis

Author

Gallagher, C. S., Mäkinen, N., Harris, H. R., Rahmioglu, N., Uimari, O., Cook, J. P., Shigesi, N., Ferreira, T., Velez-Edwards, D. R., Edwards, T. L., Mortlock, S., Ruhioglu, Z., Day, F., Becker, C. M., Karhunen, V., Martikainen, H., Järvelin, M.-R., Cantor, R. M., Ridker, P. M., Terry, K. L., Buring, J. E., Gordon, S. D., Medland, S. E., Montgomery, G. W., Nyholt, D. R., Hinds, D. A., Tung, J. Y., Perry, J. R. B., Lind, P. A., Painter, J. N., Martin, N. G., Morris, A. P., Chasman, D. I., Missmer, S. A., Zondervan, K. T., and Morton, C. C.

Published
2022
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36. Results from the Super Cryogenic Dark Matter Search (SuperCDMS) experiment at Soudan

Author

SuperCDMS Collaboration, Agnese, R., Aramaki, T., Arnquist, I. J., Baker, W., Balakishiyeva, D., Banik, S., Barker, D., Thakur, R. Basu, Bauer, D. A., Binder, T., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Caldwell, D. O., Calkins, R., Cartaro, C., Cerdeño, D. G., Chang, Y., Chen, Y., Cooley, J., Cornell, B., Cushman, P., Daal, M., Di Stefano, P. C. F., Doughty, T., Fascione, E., Figueroa-Feliciano, E., Fritts, M., Gerbier, G., Germond, R., Ghaith, M., Godfrey, G. L., Golwala, S. R., Hall, J., Harris, H. R., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Jena, C., Kelsey, M. H., Kennedy, A., Kubik, A., Kurinsky, N. A., Loer, B., Asamar, E. Lopez, Lukens, P., MacDonell, D., Mahapatra, R., Mandic, V., Mast, N., Miller, E. H., Mirabolfathi, N., Mohanty, B., Mendoza, J. D. Morales, Nelson, J., Orrell, J. L., Oser, S. M., Page, K., Page, W. A., Partridge, R., Martinez, M. Penalver, Pepin, M., Phipps, A., Poudel, S., Pyle, M., Qiu, H., Rau, W., Redl, P., Reisetter, A., Reynolds, T., Roberts, A., Robinson, A. E., Rogers, H. E., Saab, T., Sadoulet, B., Sander, J., Schneck, K., Schnee, R. W., Scorza, S., Senapati, K., Serfass, B., Speller, D., Stein, M., Street, J., Tanaka, H. A., Toback, D., Underwood, R., Villano, A. N., von Krosigk, B., Welliver, B., Wilson, J. S., Wilson, M. J., Wright, D. H., Yellin, S., Yen, J. J., Young, B. A., Zhang, X., and Zhao, X.

Subjects
High Energy Physics - Experiment, High Energy Physics - Phenomenology
Abstract

We report the result of a blinded search for Weakly Interacting Massive Particles (WIMPs) using the majority of the SuperCDMS Soudan dataset. With an exposure of 1690 kg days, a single candidate event is observed, consistent with expected backgrounds. This analysis (combined with previous Ge results) sets an upper limit on the spin-independent WIMP--nucleon cross section of $1.4 \times 10^{-44}$ ($1.0 \times 10^{-44}$) cm$^2$ at 46 GeV/$c^2$. These results set the strongest limits for WIMP--germanium-nucleus interactions for masses $>$12 GeV/$c^2$.

Published
2017
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37. Low-Mass Dark Matter Search with CDMSlite

Author

SuperCDMS Collaboration, Agnese, R., Anderson, A. J., Aralis, T., Aramaki, T., Arnquist, I. J., Baker, W., Balakishiyeva, D., Barker, D., Thakur, R. Basu, Bauer, D. A., Binder, T., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Caldwell, D. O., Calkins, R., Cartaro, C., Cerdeno, D. G., Chang, Y., Chagani, H., Chen, Y., Cooley, J., Cornell, B., Cushman, P., Daal, M., Di Stefano, P. C. F., Doughty, T., Esteban, L., Fascione, E., Figueroa-Feliciano, E., Fritts, M., Gerbier, G., Ghaith, M., Godfrey, G. L., Golwala, S. R., Hall, J., Harris, H. R., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Jena, C., Kelsey, M. H., Kennedy, A., Kubik, A., Kurinsky, N. A., Leder, A., Loer, B., Asamar, E. Lopez, Lukens, P., MacDonell, D., Mahapatra, R., Mandic, V., Mast, N., Miller, E. H., Mirabolfathi, N., Moffatt, R. A., Mohanty, B., Mendoza, J. D. Morales, Nelson, J., Orrell, J. L., Oser, S. M., Page, K., Page, W. A., Partridge, R., Pepin, M., Martinez, M. Penalver, Phipps, A., Poudel, S., Pyle, M., Qiu, H., Rau, W., Redl, P., Reisetter, A., Reynolds, T., Roberts, A., Robinson, A. E., Rogers, H. E., Saab, T., Sadoulet, B., Sander, J., Schneck, K., Schnee, R. W., Scorza, S., Senapati, K., Serfass, B., Speller, D., Stein, M., Street, J., Tanaka, H. A., Toback, D., Underwood, R., Villano, A. N., von Krosigk, B., Welliver, B., Wilson, J. S., Wilson, M. J, Wright, D. H., Yellin, S., Yen, J. J., Young, B. A., Zhang, X., and Zhao, X.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment, Physics - Instrumentation and Detectors
Abstract

The SuperCDMS experiment is designed to directly detect weakly interacting massive particles (WIMPs) that may constitute the dark matter in our Galaxy. During its operation at the Soudan Underground Laboratory, germanium detectors were run in the CDMSlite mode to gather data sets with sensitivity specifically for WIMPs with masses ${<}$10 GeV/$c^2$. In this mode, a higher detector-bias voltage is applied to amplify the phonon signals produced by drifting charges. This paper presents studies of the experimental noise and its effect on the achievable energy threshold, which is demonstrated to be as low as 56 eV$_{\text{ee}}$ (electron equivalent energy). The detector-biasing configuration is described in detail, with analysis corrections for voltage variations to the level of a few percent. Detailed studies of the electric-field geometry, and the resulting successful development of a fiducial parameter, eliminate poorly measured events, yielding an energy resolution ranging from ${\sim}$9 eV$_{\text{ee}}$ at 0 keV to 101 eV$_{\text{ee}}$ at ${\sim}$10 eV$_{\text{ee}}$. New results are derived for astrophysical uncertainties relevant to the WIMP-search limits, specifically examining how they are affected by variations in the most probable WIMP velocity and the Galactic escape velocity. These variations become more important for WIMP masses below 10 GeV/$c^2$. Finally, new limits on spin-dependent low-mass WIMP-nucleon interactions are derived, with new parameter space excluded for WIMP masses $\lesssim$3 GeV/$c^2$, Comment: 30 Pages, 33 Figures v3 to match published version in PRD. v2 contains public release (and documentation) of the CDMSlite Run 2 data as ancillary files

Published
2017
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38. Comfort with having sexual orientation recorded on official databases among a community and online sample of gay and bisexual men in Aotearoa New Zealand.

Author

Ludlam, A. H., Petousis-Harris, H., Arroll, B., and Saxton, P. J. W.

Subjects
SEXUAL orientation, CROSS-sectional method, GENDER identity, PSYCHOLOGY of LGBTQ+ people, SEXUAL orientation identity, LOGISTIC regression analysis, HUMAN sexuality, EVALUATION of medical care, DESCRIPTIVE statistics, ODDS ratio, SEX customs, ACQUISITION of data, HUMAN comfort, CONFIDENCE intervals, HEALTH equity, SEXUAL minorities, DATA analysis software
Abstract

Introduction. Sexual orientation minorities have worse health outcomes than the heterosexual majority. In 2023, Aotearoa New Zealand (NZ) added sexual and gender identity items to the Census, offering actionable data for improving sexual identity and gender identity (SOGI) community health. However, this also raises questions about individuals’ willingness to provide such information to Government and their comfort with data privacy and governance. Methods. Using data from gay, bisexual, and other men who have sex with men (GBM) participants of the Gay Auckland Periodic Sex Survey and Gay Men’s Online Sex Survey 2014 cross-sectional surveys, the study question examined comfort having their sexual orientation recorded in official databases. A logistic regression model was used to identify independent predictors of comfort, including sociodemographic and behavioural variables. Results. Of 3173 participants who completed the question, 63.1% were comfortable with recording sexual orientation. Adjusted odds ratios showed less comfort among those identifying with an ‘Other’ ethnicity (AOR: 0.64, 95% CI: 0.43–0.96), identifying as bisexual (AOR: 0.45, 95% CI: 0.35–0.56), and those who did not believe their GP to be aware of their sexuality (AOR: 0.32, 95% CI: 0.26–0.40). No sexual behaviours were independently associated with comfort. Discussion. The majority of GBM participants reported comfort with having their sexual orientation recorded on official databases, but some are not, and this is patterned by sociodemographic variables. Officials should improve the safety and perceived relevance of sexual orientation data collection efforts to increase their representativeness and utility for sexual minority populations. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2

Author

Liu, Lihong, Iketani, Sho, Guo, Yicheng, Chan, Jasper F.-W., Wang, Maple, Liu, Liyuan, Luo, Yang, Chu, Hin, Huang, Yiming, Nair, Manoj S., Yu, Jian, Chik, Kenn K.-H., Yuen, Terrence T.-T., Yoon, Chaemin, To, Kelvin K.-W., Chen, Honglin, Yin, Michael T., Sobieszczyk, Magdalena E., Huang, Yaoxing, Wang, Harris H., Sheng, Zizhang, Yuen, Kwok-Yung, and Ho, David D.

Published
2022
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41. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

Author

Brunk, Elizabeth, Chang, Roger L, Xia, Jing, Hefzi, Hooman, Yurkovich, James T, Kim, Donghyuk, Buckmiller, Evan, Wang, Harris H, Cho, Byung-Kwan, Yang, Chen, Palsson, Bernhard O, Church, George M, and Lewis, Nathan E

Subjects
Biotechnology, Human Genome, Genetics, Escherichia coli, Gene Editing, Metabolic Engineering, Prokaryotic Cells, Protein Processing, Post-Translational, Proteins, Workflow, systems biology, posttranslational modifications, metabolism, protein chemistry, omics data
Abstract

Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. Here, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coli Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.

Published
2018

42. Metagenomic mining of regulatory elements enables programmable species-selective gene expression.

Author

Johns, Nathan I, Gomes, Antonio LC, Yim, Sung Sun, Yang, Anthony, Blazejewski, Tomasz, Smillie, Christopher S, Smith, Mark B, Alm, Eric J, Kosuri, Sriram, and Wang, Harris H

Subjects
Escherichia coli, Genetic Engineering, Species Specificity, Gene Expression Regulation, Regulatory Elements, Transcriptional, Metabolic Networks and Pathways, Metagenomics, Data Mining, Synthetic Biology, Metabolic Engineering, Regulatory Elements, Transcriptional, Developmental Biology, Biological Sciences, Technology, Medical and Health Sciences
Abstract

Robust and predictably performing synthetic circuits rely on the use of well-characterized regulatory parts across different genetic backgrounds and environmental contexts. Here we report the large-scale metagenomic mining of thousands of natural 5' regulatory sequences from diverse bacteria, and their multiplexed gene expression characterization in industrially relevant microbes. We identified sequences with broad and host-specific expression properties that are robust in various growth conditions. We also observed substantial differences between species in terms of their capacity to utilize exogenous regulatory sequences. Finally, we demonstrate programmable species-selective gene expression that produces distinct and diverse output patterns in different microbes. Together, these findings provide a rich resource of characterized natural regulatory sequences and a framework that can be used to engineer synthetic gene circuits with unique and tunable cross-species functionality and properties, and also suggest the prospect of ultimately engineering complex behaviors at the community level.

Published
2018

43. Lectures on the Philosophy of Religion : The Lectures of 1827

Author

HEGEL, GEORG WILHELM FRIEDRICH, Hodgson, Peter C., Edited by, Brown, R. F., Hodgson, P. C., Stewart, J. M., Harris, H. S., with the assistance of, HEGEL, GEORG WILHELM FRIEDRICH, Hodgson, Peter C., Brown, R. F., Hodgson, P. C., Stewart, J. M., and Harris, H. S.

Published
2023

44. SARS-CoV-2 Omicron BA.2.87.1 Exhibits Higher Susceptibility to Serum Neutralization Than EG.5.1 and JN.1

Author

Wang, Qian, primary, Guo, Yicheng, additional, Schwanz, Logan T., additional, Mellis, Ian A., additional, Sun, Yiwei, additional, Qu, Yiming, additional, Urtecho, Guillaume, additional, Valdez, Riccardo, additional, Stoneman, Emily, additional, Gordon, Aubree, additional, Wang, Harris H., additional, Ho, David D., additional, and Liu, Lihong, additional

Published
2024
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46. Projected Sensitivity of the SuperCDMS SNOLAB experiment

Author

Agnese, R., Anderson, A. J., Aramaki, T., Arnquist, I., Baker, W., Barker, D., Thakur, R. Basu, Bauer, D. A., Borgland, A., Bowles, M. A., Brink, P. L., Bunker, R., Cabrera, B., Caldwell, D. O., Calkins, R., Cartaro, C., Cerdeño, D. G., Chagani, H., Chen, Y., Cooley, J., Cornell, B., Cushman, P., Daal, M., Di Stefano, P. C. F., Doughty, T., Esteban, L., Fallows, S., Figueroa-Feliciano, E., Fritts, M., Gerbier, G., Ghaith, M., Godfrey, G. L., Golwala, S. R., Hall, J., Harris, H. R., Hofer, T., Holmgren, D., Hong, Z., Hoppe, E., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Jastram, A., Kelsey, M. H., Kennedy, A., Kubik, A., Kurinsky, N. A., Leder, A., Loer, B., Asamar, E. Lopez, Lukens, P., Mahapatra, R., Mandic, V., Mast, N., Mirabolfathi, N., Moffatt, R. A., Mendoza, J. D. Morales, Orrell, J. L., Oser, S. M., Page, K., Page, W. A., Partridge, R., Pepin, M., Phipps, A., Poudel, S., Pyle, M., Qiu, H., Rau, W., Redl, P., Reisetter, A., Roberts, A., Robinson, A. E., Rogers, H. E., Saab, T., Sadoulet, B., Sander, J., Schneck, K., Schnee, R. W., Serfass, B., Speller, D., Stein, M., Street, J., Tanaka, H. A., Toback, D., Underwood, R., Villano, A. N., von Krosigk, B., Welliver, B., Wilson, J. S., Wright, D. H., Yellin, S., Yen, J. J., Young, B. A., Zhang, X., and Zhao, X.

Subjects
Physics - Instrumentation and Detectors, Astrophysics - Cosmology and Nongalactic Astrophysics, High Energy Physics - Experiment
Abstract

SuperCDMS SNOLAB will be a next-generation experiment aimed at directly detecting low-mass (< 10 GeV/c$^2$) particles that may constitute dark matter by using cryogenic detectors of two types (HV and iZIP) and two target materials (germanium and silicon). The experiment is being designed with an initial sensitivity to nuclear recoil cross sections ~ 1 x 10$^{-43}$ cm$^2$ for a dark matter particle mass of 1 GeV/c$^2$, and with capacity to continue exploration to both smaller masses and better sensitivities. The phonon sensitivity of the HV detectors will be sufficient to detect nuclear recoils from sub-GeV dark matter. A detailed calibration of the detector response to low energy recoils will be needed to optimize running conditions of the HV detectors and to interpret their data for dark matter searches. Low-activity shielding, and the depth of SNOLAB, will reduce most backgrounds, but cosmogenically produced $^{3}$H and naturally occurring $^{32}$Si will be present in the detectors at some level. Even if these backgrounds are x10 higher than expected, the science reach of the HV detectors would be over three orders of magnitude beyond current results for a dark matter mass of 1 GeV/c$^2$. The iZIP detectors are relatively insensitive to variations in detector response and backgrounds, and will provide better sensitivity for dark matter particle masses (> 5 GeV/c$^2$). The mix of detector types (HV and iZIP), and targets (germanium and silicon), planned for the experiment, as well as flexibility in how the detectors are operated, will allow us to maximize the low-mass reach, and understand the backgrounds that the experiment will encounter. Upgrades to the experiment, perhaps with a variety of ultra-low-background cryogenic detectors, will extend dark matter sensitivity down to the "neutrino floor", where coherent scatters of solar neutrinos become a limiting background., Comment: SuperCDMS SNOLAB Projected sensitivity reach

Published
2016
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47. Background Studies for the MINER Coherent Neutrino Scattering Reactor Experiment

Author

MINER Collaboration, Agnolet, G., Baker, W., Barker, D., Beck, R., Carroll, T. J., Cesar, J., Cushman, P., Dent, J. B., De Rijck, S., Dutta, B., Flanagan, W., Fritts, M., Gao, Y., Harris, H. R., Hays, C. C., Iyer, V., Jastram, A., Kadribasic, F., Kennedy, A., Kubik, A., Ogawa, I., Lang, K., Mahapatra, R., Mandic, V., Martin, R. D., Mast, N., McDeavitt, S., Mirabolfathi, N., Mohanty, B., Nakajima, K., Newhouse, J., Newstead, J. L., Phan, D., Proga, M., Roberts, A., Rogachev, G., Salazar, R., Sander, J., Senapati, K., Shimada, M., Strigari, L., Tamagawa, Y., Teizer, W., Vermaak, J. I. C., Villano, A. N., Walker, J., Webb, B., Wetzel, Z., and Yadavalli, S. A.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

The proposed Mitchell Institute Neutrino Experiment at Reactor (MINER) experiment at the Nuclear Science Center at Texas A&M University will search for coherent elastic neutrino-nucleus scattering within close proximity (about 2 meters) of a 1 MW TRIGA nuclear reactor core using low threshold, cryogenic germanium and silicon detectors. Given the Standard Model cross section of the scattering process and the proposed experimental proximity to the reactor, as many as 5 to 20 events/kg/day are expected. We discuss the status of preliminary measurements to characterize the main backgrounds for the proposed experiment. Both in situ measurements at the experimental site and simulations using the MCNP and GEANT4 codes are described. A strategy for monitoring backgrounds during data taking is briefly discussed., Comment: 12 pages, 14 figures

Published
2016

49. COVID-19 vaccines and adverse events of special interest: A multinational Global Vaccine Data Network (GVDN) cohort study of 99 million vaccinated individuals

Author

Faksova, K, Walsh, D, Jiang, Y, Griffin, J, Phillips, A, Gentile, A, Kwong, JC, Macartney, K, Naus, M, Grange, Z, Escolano, S, Sepulveda, G, Shetty, A, Pillsbury, A, Sullivan, C, Naveed, Z, Janjua, NZ, Giglio, N, Perala, J, Nasreen, S, Gidding, H, Hovi, P, Vo, T, Cui, F, Deng, L, Cullen, L, Artama, M, Lu, H, Clothier, HJ, Batty, K, Paynter, J, Petousis-Harris, H, Buttery, J, Black, S, Hviid, A, Faksova, K, Walsh, D, Jiang, Y, Griffin, J, Phillips, A, Gentile, A, Kwong, JC, Macartney, K, Naus, M, Grange, Z, Escolano, S, Sepulveda, G, Shetty, A, Pillsbury, A, Sullivan, C, Naveed, Z, Janjua, NZ, Giglio, N, Perala, J, Nasreen, S, Gidding, H, Hovi, P, Vo, T, Cui, F, Deng, L, Cullen, L, Artama, M, Lu, H, Clothier, HJ, Batty, K, Paynter, J, Petousis-Harris, H, Buttery, J, Black, S, and Hviid, A

Abstract

BACKGROUND: The Global COVID Vaccine Safety (GCoVS) Project, established in 2021 under the multinational Global Vaccine Data Network™ (GVDN®), facilitates comprehensive assessment of vaccine safety. This study aimed to evaluate the risk of adverse events of special interest (AESI) following COVID-19 vaccination from 10 sites across eight countries. METHODS: Using a common protocol, this observational cohort study compared observed with expected rates of 13 selected AESI across neurological, haematological, and cardiac outcomes. Expected rates were obtained by participating sites using pre-COVID-19 vaccination healthcare data stratified by age and sex. Observed rates were reported from the same healthcare datasets since COVID-19 vaccination program rollout. AESI occurring up to 42 days following vaccination with mRNA (BNT162b2 and mRNA-1273) and adenovirus-vector (ChAdOx1) vaccines were included in the primary analysis. Risks were assessed using observed versus expected (OE) ratios with 95 % confidence intervals. Prioritised potential safety signals were those with lower bound of the 95 % confidence interval (LBCI) greater than 1.5. RESULTS: Participants included 99,068,901 vaccinated individuals. In total, 183,559,462 doses of BNT162b2, 36,178,442 doses of mRNA-1273, and 23,093,399 doses of ChAdOx1 were administered across participating sites in the study period. Risk periods following homologous vaccination schedules contributed 23,168,335 person-years of follow-up. OE ratios with LBCI > 1.5 were observed for Guillain-Barré syndrome (2.49, 95 % CI: 2.15, 2.87) and cerebral venous sinus thrombosis (3.23, 95 % CI: 2.51, 4.09) following the first dose of ChAdOx1 vaccine. Acute disseminated encephalomyelitis showed an OE ratio of 3.78 (95 % CI: 1.52, 7.78) following the first dose of mRNA-1273 vaccine. The OE ratios for myocarditis and pericarditis following BNT162b2, mRNA-1273, and ChAdOx1 were significantly increased with LBCIs > 1.5. CONCLUSION: This multi-country a

Published
2024

50. COVID-19 vaccines and adverse events of special interest:A multinational Global Vaccine Data Network (GVDN) cohort study of 99 million vaccinated individuals

Author

Faksova, K., Walsh, D., Jiang, Y., Griffin, J., Phillips, A., Gentile, A., Kwong, J. C., Macartney, K., Naus, M., Grange, Z., Escolano, S., Sepulveda, G., Shetty, A., Pillsbury, A., Sullivan, C., Naveed, Z., Janjua, N. Z., Giglio, N., Perälä, J., Nasreen, S., Gidding, H., Hovi, P., Vo, T., Cui, F., Deng, L., Cullen, L., Artama, M., Weintraub, E., Lu, H., Clothier, H. J., Batty, K., Paynter, J., Petousis-Harris, H., Buttery, J., Black, S., Hviid, A., Faksova, K., Walsh, D., Jiang, Y., Griffin, J., Phillips, A., Gentile, A., Kwong, J. C., Macartney, K., Naus, M., Grange, Z., Escolano, S., Sepulveda, G., Shetty, A., Pillsbury, A., Sullivan, C., Naveed, Z., Janjua, N. Z., Giglio, N., Perälä, J., Nasreen, S., Gidding, H., Hovi, P., Vo, T., Cui, F., Deng, L., Cullen, L., Artama, M., Weintraub, E., Lu, H., Clothier, H. J., Batty, K., Paynter, J., Petousis-Harris, H., Buttery, J., Black, S., and Hviid, A.

Abstract

Background: The Global COVID Vaccine Safety (GCoVS) Project, established in 2021 under the multinational Global Vaccine Data Network™ (GVDN®), facilitates comprehensive assessment of vaccine safety. This study aimed to evaluate the risk of adverse events of special interest (AESI) following COVID-19 vaccination from 10 sites across eight countries. Methods: Using a common protocol, this observational cohort study compared observed with expected rates of 13 selected AESI across neurological, haematological, and cardiac outcomes. Expected rates were obtained by participating sites using pre-COVID-19 vaccination healthcare data stratified by age and sex. Observed rates were reported from the same healthcare datasets since COVID-19 vaccination program rollout. AESI occurring up to 42 days following vaccination with mRNA (BNT162b2 and mRNA-1273) and adenovirus-vector (ChAdOx1) vaccines were included in the primary analysis. Risks were assessed using observed versus expected (OE) ratios with 95 % confidence intervals. Prioritised potential safety signals were those with lower bound of the 95 % confidence interval (LBCI) greater than 1.5. Results: Participants included 99,068,901 vaccinated individuals. In total, 183,559,462 doses of BNT162b2, 36,178,442 doses of mRNA-1273, and 23,093,399 doses of ChAdOx1 were administered across participating sites in the study period. Risk periods following homologous vaccination schedules contributed 23,168,335 person-years of follow-up. OE ratios with LBCI > 1.5 were observed for Guillain-Barré syndrome (2.49, 95 % CI: 2.15, 2.87) and cerebral venous sinus thrombosis (3.23, 95 % CI: 2.51, 4.09) following the first dose of ChAdOx1 vaccine. Acute disseminated encephalomyelitis showed an OE ratio of 3.78 (95 % CI: 1.52, 7.78) following the first dose of mRNA-1273 vaccine. The OE ratios for myocarditis and pericarditis following BNT162b2, mRNA-1273, and ChAdOx1 were significantly increased with LBCIs > 1.5. Conclusion: This multi

Published
2024

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