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Start Over Journal scientific reports Publisher nature research
5 results

1. Reconstructing and counting genomic fragments through tagmentation-based haploid phasing

Author

Leong, Patrick P. T., Mihajlović, Aleksandar, Bogdanović, Nadežda, Breberina, Luka M., Xi, Larry, Leong, Patrick P. T., Mihajlović, Aleksandar, Bogdanović, Nadežda, Breberina, Luka M., and Xi, Larry

Abstract

Single-cell sequencing provides a new level of granularity in studying the heterogeneous nature of cancer cells. For some cancers, this heterogeneity is the result of copy number changes of genes within the cellular genomes. The ability to accurately determine such copy number changes is critical in tracing and understanding tumorigenesis. Current single-cell genome sequencing methodologies infer copy numbers based on statistical approaches followed by rounding decimal numbers to integer values. Such methodologies are sample dependent, have varying calling sensitivities which heavily depend on the sample’s ploidy and are sensitive to noise in sequencing data. In this paper we have demonstrated the concept of integer-counting by using a novel bioinformatic algorithm built on our library construction chemistry in order to detect the discrete nature of the genome.

Published
2021

2. Lives versus Livelihoods? Perceived economic risk has a stronger association with support for COVID-19 preventive measures than perceived health risk

Author

Nisa, C.F., Bélanger, J.J., Faller, D.G., Buttrick, N.R., Mierau, J.O., Austin, M.M.K., Schumpe, B.M., Sasin, E.M., Agostini, M., Gützkow, B., Kreienkamp, J., Abakoumkin, G., Abdul Khaiyom, J.H., Ahmedi, V., Akkas, H., Almenara, C.A., Atta, M., Bagci, S.C., Basel, S., Kida, E.B., Bernardo, A.B.I., Chobthamkit, P., Choi, H.-S., Cristea, M., Csaba, S., Damnjanović, Kaja, Danyliuk, I., Dash, A., Di Santo, D., Douglas, K.M., Enea, V., Fitzsimons, G., Gheorghiu, A., Gómez, Á., Grzymala-Moszczynska, J., Hamaidia, A., Han, Q., Helmy, M., Hudiyana, J., Jeronimus, B.F., Jiang, D.-Y., Jovanović, V., Kamenov, Ž., Kende, Anna, Keng, S.-L., Kieu, T.T.T., Koc, Y., Kovyazina, K., Kozytska, I., Krause, J., Kruglanski, A.W., Kurapov, A., Kutlaca, M., Lantos, Nora Anna, Lemay, E.P., Lesmana, C.B.J., Louis, W.R., Lueders, A., Malik, N.I., Martinez, A., McCabe, K.O., Mehulić, J., Milla, M.N., Mohammed, I., Molinario, E., Moyano, M., Muhammad, H., Mula, S., Muluk, H., Myroniuk, S., Najafi, R., Nyúl, B., O’Keefe, P.A., Osuna, J.J.O., Osin, E.N., Park, J., Pica, G., Pierro, A., Rees, J., Reitsema, A.M., Resta, E., Rullo, M., Ryan, M.K., Samekin, A., Santtila, P., Selim, Heyla A., Stanton, M.V., Sultana, S., Sutton, R.M., Tseliou, E., Utsugi, A., van Breen, J.A., Van Lissa, C.J., Van Veen, K., vanDellen, M.R., Vázquez, A., Wollast, R., Yeung, V.W.-L., Zand, S., Žeželj, Iris, Zheng, B., Zick, A., Zúñiga, C., Leander, N.P., Nisa, C.F., Bélanger, J.J., Faller, D.G., Buttrick, N.R., Mierau, J.O., Austin, M.M.K., Schumpe, B.M., Sasin, E.M., Agostini, M., Gützkow, B., Kreienkamp, J., Abakoumkin, G., Abdul Khaiyom, J.H., Ahmedi, V., Akkas, H., Almenara, C.A., Atta, M., Bagci, S.C., Basel, S., Kida, E.B., Bernardo, A.B.I., Chobthamkit, P., Choi, H.-S., Cristea, M., Csaba, S., Damnjanović, Kaja, Danyliuk, I., Dash, A., Di Santo, D., Douglas, K.M., Enea, V., Fitzsimons, G., Gheorghiu, A., Gómez, Á., Grzymala-Moszczynska, J., Hamaidia, A., Han, Q., Helmy, M., Hudiyana, J., Jeronimus, B.F., Jiang, D.-Y., Jovanović, V., Kamenov, Ž., Kende, Anna, Keng, S.-L., Kieu, T.T.T., Koc, Y., Kovyazina, K., Kozytska, I., Krause, J., Kruglanski, A.W., Kurapov, A., Kutlaca, M., Lantos, Nora Anna, Lemay, E.P., Lesmana, C.B.J., Louis, W.R., Lueders, A., Malik, N.I., Martinez, A., McCabe, K.O., Mehulić, J., Milla, M.N., Mohammed, I., Molinario, E., Moyano, M., Muhammad, H., Mula, S., Muluk, H., Myroniuk, S., Najafi, R., Nyúl, B., O’Keefe, P.A., Osuna, J.J.O., Osin, E.N., Park, J., Pica, G., Pierro, A., Rees, J., Reitsema, A.M., Resta, E., Rullo, M., Ryan, M.K., Samekin, A., Santtila, P., Selim, Heyla A., Stanton, M.V., Sultana, S., Sutton, R.M., Tseliou, E., Utsugi, A., van Breen, J.A., Van Lissa, C.J., Van Veen, K., vanDellen, M.R., Vázquez, A., Wollast, R., Yeung, V.W.-L., Zand, S., Žeželj, Iris, Zheng, B., Zick, A., Zúñiga, C., and Leander, N.P.

Abstract

This paper examines whether compliance with COVID-19 mitigation measures is motivated by wanting to save lives or save the economy (or both), and which implications this carries to fight the pandemic. National representative samples were collected from 24 countries (N = 25,435). The main predictors were (1) perceived risk to contract coronavirus, (2) perceived risk to suffer economic losses due to coronavirus, and (3) their interaction effect. Individual and country-level variables were added as covariates in multilevel regression models. We examined compliance with various preventive health behaviors and support for strict containment policies. Results show that perceived economic risk consistently predicted mitigation behavior and policy support—and its effects were positive. Perceived health risk had mixed effects. Only two significant interactions between health and economic risk were identified—both positive.

Published
2021

3. Author Correction: Fish proliferation and rare-earth deposition by topographically induced upwelling at the late Eocene cooling event (Scientific Reports, (2020), 10, 1, (9896), 10.1038/s41598-020-66835-8)

Author

Ohta, Junichiro, Yasukawa, Kazutaka, Nozaki, Tatsuo, Takaya, Yutaro, Mimura, Kazuhide, Fujinaga, Koichiro, Nakamura, Kentaro, Usui, Yoichi, Kimura, Jun-ichi, Chang, Qing, and Kato, Yasuhiro

Abstract

金沢大学理工研究域地球社会基盤学系, An amendment to this paper has been published and can be accessed via a link at the top of the paper. © 2020, The Author(s).

Published
2020

4. Classes of low-frequency earthquakes based on inter-time distribution reveal a precursor event for the 2011 Great Tohoku Earthquake

Author

Tomoki Tokuda and Hirohiko Shimada

Subjects
0301 basic medicine, FOS: Computer and information sciences, Science, Generalized gamma distribution, Time distribution, FOS: Physical sciences, Low frequency, Statistics - Applications, Article, Physics - Geophysics, 03 medical and health sciences, 0302 clinical medicine, Large earthquakes, Statistical analysis, Applications (stat.AP), Condensed Matter - Statistical Mechanics, Seismology, Mathematics, Event (probability theory), Multidisciplinary, Statistical Mechanics (cond-mat.stat-mech), Applied mathematics, Geophysics (physics.geo-ph), 030104 developmental biology, Medicine, 030217 neurology & neurosurgery
Abstract

Recently, slow earthquakes (slow EQ) have received much attention relative to understanding the mechanisms underlying large earthquakes and to detecting their precursors. Low-frequency earthquakes (LFE) are a specific type of slow EQ. In the present paper, we reveal the relevance of LFEs to the 11 March 2011 Great Tohoku Earthquake (Tohoku-oki EQ) by means of cluster analysis. We classified LFEs in northern Japan in a data-driven manner, based on inter-time, the time interval between neighboring LFEs occurring within 10 km. We found that there are four classes of LFE that are characterized by median inter-times of 24 seconds, 27 minutes, 2.0 days, and 35 days, respectively. Remarkably, in examining the relevance of these classes to the Tohoku-oki EQ, we found that activity in the shortest inter-time class (median 24 seconds) diminished significantly at least three months before the Tohoku-oki EQ, and became completely quiescent 30 days before the event (p-value = 0.00014). Further statistical analysis implies that this class, together with a similar class of volcanic tremor, may have served as a precursor of the Tohoku-oki EQ. We discuss a generative model for these classes of LFE, in which the shortest inter-time class is characterized by a generalized gamma distribution with the product of shape parameters vκ = 1:54 in the domain of inter-time close to zero. We give a possible geodetic interpretation for the relevance of LFE to the Tohoku-oki EQ.

Published
2019

5. Quantitative Evaluation of Pain during Electrocutaneous Stimulation using a Log-Linearized Peripheral Arterial Viscoelastic Model

Author

Takafumi Sasaoka, Harutoyo Hirano, Noboru Saeki, Atsuo Yoshino, Shigeto Yamawaki, Toshio Tsuji, Ryuji Nakamura, Masashi Kawamoto, Hiroki Matsubara, Hiroki Hirano, Masao Yoshizumi, and Zu Soh

Subjects
0301 basic medicine, Adult, Male, medicine.medical_specialty, Sympathetic Nervous System, Visual analogue scale, Pain, lcsh:Medicine, Blood Pressure, Article, 03 medical and health sciences, Electrocardiography, 0302 clinical medicine, Vascular Stiffness, Internal medicine, medicine, Numeric Rating Scale, Humans, 030212 general & internal medicine, Peripheral Nerves, Photoplethysmography, lcsh:Science, Pain Measurement, Multidisciplinary, medicine.diagnostic_test, business.industry, lcsh:R, Blood Pressure Determination, Pain Perception, Sigmoid function, Arteries, Models, Theoretical, medicine.disease, Intensity (physics), Peripheral, 030104 developmental biology, Blood pressure, Cardiology, Arterial stiffness, lcsh:Q, business
Abstract

In clinical practice, subjective pain evaluations, e.g., the visual analogue scale and the numeric rating scale, are generally employed, but these are limited in terms of their ability to detect inaccurate reports, and are unsuitable for use in anesthetized patients or those with dementia. We focused on the peripheral sympathetic nerve activity that responds to pain, and propose a method for evaluating pain sensation, including intensity, sharpness, and dullness, using the arterial stiffness index. In the experiment, electrocardiogram, blood pressure, and photoplethysmograms were obtained, and an arterial viscoelastic model was applied to estimate arterial stiffness. The relationships among the stiffness index, self-reported pain sensation, and electrocutaneous stimuli were examined and modelled. The relationship between the stiffness index and pain sensation could be modelled using a sigmoid function with high determination coefficients, where R2 ≥ 0.88, p, This work was supported by the Center of Innovation Program from Japan Science and Technology Agency., Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-21223-1.

Published
2018