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1. The SEDIGISM survey: first data release and overview of the Galactic structure

Author

Schuller, F., Urquhart, J. S., Csengeri, T., Colombo, D., Duarte-Cabral, A., Mattern, M., Ginsburg, A., Pettitt, A. R., Wyrowski, F., Anderson, L., Azagra, F., Barnes, P., Beltran, M., Beuther, H., Billington, S., Bronfman, L., Cesaroni, R., Dobbs, C., Eden, D., Lee, M. -Y., Medina, S. -N. X., Menten, K. M., Moore, T., Montenegro-Montes, F. M., Ragan, S., Rigby, A., Riener, M., Russeil, D., Schisano, E., Sanchez-Monge, A., Traficante, A., Zavagno, A., Agurto, C., Bontemps, S., Finger, R., Giannetti, A., Gonzalez, E., Hernandez, A. K., Henning, T., Kainulainen, J., Kauffmann, J., Leurini, S., Lopez, S., Mac-Auliffe, F., Mazumdar, P., Molinari, S., Motte, F., Muller, E., Nguyen-Luong, Q., Parra, R., Perez-Beaupuits, J. -P., Schilke, P., Schneider, N., Suri, S., Testi, L., Torstensson, K., Veena, V. S., Venegas, P., Wang, K., and Wienen, M.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

The SEDIGISM (Structure, Excitation and Dynamics of the Inner Galactic Interstellar Medium) survey used the APEX telescope to map 84 deg^2 of the Galactic plane between l = -60 deg and l = +31 deg in several molecular transitions, including 13CO(2-1) and C18O(2-1), thus probing the moderately dense (~10^3 cm^-3) component of the interstellar medium. With an angular resolution of 30'' and a typical 1-sigma sensitivity of 0.8-1.0 K at 0.25 km/s velocity resolution, it gives access to a wide range of structures, from individual star-forming clumps to giant molecular clouds and complexes. The coverage includes a good fraction of the first and fourth Galactic quadrants, allowing us to constrain the large scale distribution of cold molecular gas in the inner Galaxy. In this paper we provide an updated overview of the full survey and the data reduction procedures used. We also assess the quality of these data and describe the data products that are being made publicly available as part of this first data release (DR1). We present integrated maps and position-velocity maps of the molecular gas and use these to investigate the correlation between the molecular gas and the large scale structural features of the Milky Way such as the spiral arms, Galactic bar and Galactic centre. We find that approximately 60 per cent of the molecular gas is associated with the spiral arms and these appear as strong intensity peaks in the derived Galactocentric distribution. We also find strong peaks in intensity at specific longitudes that correspond to the Galactic centre and well known star forming complexes, revealing that the 13CO emission is concentrated in a small number of complexes rather than evenly distributed along spiral arms., Comment: MNRAS, in press

Published
2020
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2. The SEDIGISM survey: Molecular clouds in the inner Galaxy

Author

Duarte-Cabral, A., Colombo, D., Urquhart, J. S., Ginsburg, A., Russeil, D., Schuller, F., Anderson, L. D., Barnes, P. J., Beltran, M. T., Beuther, H., Bontemps, S., Bronfman, L., Csengeri, T., Dobbs, C. L., Eden, D., Giannetti, A., Kauffmann, J., Mattern, M., Medina, S. -N. X., Menten, K. M., Lee, M. -Y., Pettitt, A. R., Riener, M., Rigby, A. J., Trafficante, A., Veena, V. S., Wienen, M., Wyrowski, F., Agurto, C., Azagra, F., Cesaroni, R., Finger, R., Gonzalez, E., Henning, T., Hernandez, A. K., Kainulainen, J., Leurini, S., Lopez, S., Mac-Auliffe, F., Mazumdar, P., Molinari, S., Motte, F., Muller, E., Nguyen-Luong, Q., Parra, R., Perez-Beaupuits, J. -P., Montenegro-Montes, F. M., Moore, T. J. T., Ragan, S. E., Sanchez-Monge, A., Sanna, A., Schilke, P., Schisano, E., Schneider, N., Suri, S., Testi, L., Torstensson, K., Venegas, P., Wang, K., and Zavagno, A.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

We use the 13CO(2-1) emission from the SEDIGISM high-resolution spectral-line survey of the inner Galaxy, to extract the molecular cloud population with a large dynamic range in spatial scales, using the SCIMES algorithm. This work compiles a cloud catalogue with a total of 10663 molecular clouds, 10300 of which we were able to assign distances and compute physical properties. We study some of the global properties of clouds using a science sample, consisting of 6664 well resolved sources and for which the distance estimates are reliable. In particular, we compare the scaling relations retrieved from SEDIGISM to those of other surveys, and we explore the properties of clouds with and without high-mass star formation. Our results suggest that there is no single global property of a cloud that determines its ability to form massive stars, although we find combined trends of increasing mass, size, surface density and velocity dispersion for the sub-sample of clouds with ongoing high-mass star formation. We then isolate the most extreme clouds in the SEDIGISM sample (i.e. clouds in the tails of the distributions) to look at their overall Galactic distribution, in search for hints of environmental effects. We find that, for most properties, the Galactic distribution of the most extreme clouds is only marginally different to that of the global cloud population. The Galactic distribution of the largest clouds, the turbulent clouds and the high-mass star-forming clouds are those that deviate most significantly from the global cloud population. We also find that the least dynamically active clouds (with low velocity dispersion or low virial parameter) are situated further afield, mostly in the least populated areas. However, we suspect that part of these trends may be affected by some observational biases, and thus require further follow up work in order to be confirmed., Comment: 25 pages (+ appendices, 15 pages), 26 figures, MNRAS

Published
2020
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3. SEDIGISM: Structure, excitation, and dynamics of the inner Galactic interstellar medium

Author

Schuller, F., Csengeri, T., Urquhart, J. S., Duarte-Cabral, A., Barnes, P. J., Giannetti, A., Hernandez, A. K., Leurini, S., Mattern, M., Medina, S. -N. X., Agurto, C., Azagra, F., Anderson, L. D., Beltrán, M. T., Beuther, H., Bontemps, S., Bronfman, L., Dobbs, C. L., Dumke, M., Finger, R., Ginsburg, A., Gonzalez, E., Henning, T., Kauffmann, J., Mac-Auliffe, F., Menten, K. M., Montenegro-Montes, F. M., Moore, T. J. T., Muller, E., Parra, R., Perez-Beaupuits, J. -P., Pettitt, A., Russeil, D., Sánchez-Monge, Á., Schilke, P., Schisano, E., Suri, S., Testi, L., Torstensson, K., Venegas, P., Wang, K., Wienen, M., Wyrowski, F., and Zavagno, A.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

The origin and life-cycle of molecular clouds are still poorly constrained, despite their importance for understanding the evolution of the interstellar medium. We have carried out a systematic, homogeneous, spectroscopic survey of the inner Galactic plane, in order to complement the many continuum Galactic surveys available with crucial distance and gas-kinematic information. Our aim is to combine this data set with recent infrared to sub-millimetre surveys at similar angular resolutions. The SEDIGISM survey covers 78 deg^2 of the inner Galaxy (-60 deg < l < +18 deg, |b| < 0.5 deg) in the J=2-1 rotational transition of 13CO. This isotopologue of CO is less abundant than 12CO by factors up to 100. Therefore, its emission has low to moderate optical depths, and higher critical density, making it an ideal tracer of the cold, dense interstellar medium. The data have been observed with the SHFI single-pixel instrument at APEX. The observational setup covers the 13CO(2-1) and C18O(2-1) lines, plus several transitions from other molecules. The observations have been completed. Data reduction is in progress, and the final data products will be made available in the near future. Here we give a detailed description of the survey and the dedicated data reduction pipeline. Preliminary results based on a science demonstration field covering -20 deg < l < -18.5 deg are presented. Analysis of the 13CO(2-1) data in this field reveals compact clumps, diffuse clouds, and filamentary structures at a range of heliocentric distances. By combining our data with data in the (1-0) transition of CO isotopologues from the ThrUMMS survey, we are able to compute a 3D realization of the excitation temperature and optical depth in the interstellar medium. Ultimately, this survey will provide a detailed, global view of the inner Galactic interstellar medium at an unprecedented angular resolution of ~30"., Comment: 30 pages. Accepted for publication in A&A. Abstract slightly shortened due to arXiv requirements

Published
2017
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4. Accelerating Medicines Partnership® Schizophrenia (AMP® SCZ): Rationale and Study Design of the Largest Global Prospective Cohort Study of Clinical High Risk for Psychosis

Author

Wannan, CMJ, Nelson, B, Addington, J, Allott, K, Anticevic, A, Arango, C, Baker, JT, Bearden, CE, Billah, T, Bouix, S, Broome, MR, Buccilli, K, Cadenhead, KS, Calkins, ME, Cannon, TD, Cecci, G, Chen, EYH, Cho, KIK, Choi, J, Clark, SR, Coleman, MJ, Conus, P, Corcoran, CM, Cornblatt, BA, Diaz-Caneja, CM, Dwyer, D, Ebdrup, BH, Ellman, LM, Fusar-Poli, P, Galindo, L, Gaspar, PA, Gerber, C, Glenthoj, LB, Glynn, R, Harms, MP, Horton, LE, Kahn, RS, Kambeitz, J, Kambeitz-Ilankovic, L, Kane, JM, Kapur, T, Keshavan, MS, Kim, S-W, Koutsouleris, N, Kubicki, M, Kwon, JS, Langbein, K, Lewandowski, KE, Light, GA, Mamah, D, Marcy, PJ, Mathalon, DH, McGorry, PD, Mittal, VA, Nordentoft, M, Nunez, A, Pasternak, O, Pearlson, GD, Perez, J, Perkins, DO, Powers, AR, Roalf, DR, Sabb, FW, Schiffman, J, Shah, JL, Smesny, S, Spark, J, Stone, WS, Strauss, GP, Tamayo, Z, Torous, J, Upthegrove, R, Vangel, M, Verma, S, Wang, J, Winter-van Rossum, I, Wolf, DH, Wolff, P, Wood, SJ, Yung, AR, Agurto, C, Alvarez-Jimenez, M, Amminger, P, Armando, M, Asgari-Targhi, A, Cahill, J, Carrion, RE, Castro, E, Cetin-Karayumak, S, Chakravarty, MM, Cho, YT, Cotter, D, D'Alfonso, S, Ennis, M, Fadnavis, S, Fonteneau, C, Gao, C, Gupta, T, Gur, RE, Gur, RC, Hamilton, HK, Hoftman, GD, Jacobs, GR, Jarcho, J, Ji, JL, Kohler, CG, Lalousis, PA, Lavoie, S, Lepage, M, Liebenthal, E, Mervis, J, Murty, V, Nicholas, SC, Ning, L, Penzel, N, Poldrack, R, Polosecki, P, Pratt, DN, Rabin, R, Eichi, HR, Rathi, Y, Reichenberg, A, Reinen, J, Rogers, J, Ruiz-Yu, B, Scott, I, Seitz-Holland, J, Srihari, VH, Srivastava, A, Thompson, A, Turetsky, BI, Walsh, BC, Whitford, T, Wigman, JTW, Yao, B, Yuen, HP, Ahmed, U, Byun, AJS, Chung, Y, Do, K, Hendricks, L, Huynh, K, Jeffries, C, Lane, E, Langholm, C, Lin, E, Mantua, V, Santorelli, G, Ruparel, K, Zoupou, E, Adasme, T, Addamo, L, Adery, L, Ali, M, Auther, A, Aversa, S, Baek, S-H, Bates, K, Bathery, A, Bayer, JMM, Beedham, R, Bilgrami, Z, Birch, S, Bonoldi, I, Borders, O, Borgatti, R, Brown, L, Bruna, A, Carrington, H, Castillo-Passi, RI, Chen, J, Cheng, N, Ching, AE, Clifford, C, Colton, B-L, Contreras, P, Corral, S, Damiani, S, Done, M, Estrade, A, Etuka, BA, Formica, M, Furlan, R, Geljic, M, Germano, C, Getachew, R, Goncalves, M, Haidar, A, Hartmann, J, Jo, A, John, O, Kerins, S, Kerr, M, Kesselring, I, Kim, H, Kim, N, Kinney, K, Krcmar, M, Kotler, E, Lafanechere, M, Lee, C, Llerena, J, Markiewicz, C, Matnejl, P, Maturana, A, Mavambu, A, Mayol-Troncoso, R, McDonnell, A, McGowan, A, McLaughlin, D, McIlhenny, R, McQueen, B, Mebrahtu, Y, Mensi, M, Hui, CLM, Suen, YN, Wong, SMY, Morrell, N, Omar, M, Partridge, A, Phassouliotis, C, Pichiecchio, A, Politi, P, Porter, C, Provenzani, U, Prunier, N, Raj, J, Ray, S, Rayner, V, Reyes, M, Reynolds, K, Rush, S, Salinas, C, Shetty, J, Snowball, C, Tod, S, Turra-Farina, G, Valle, D, Veale, S, Whitson, S, Wickham, A, Youn, S, Zamorano, F, Zavaglia, E, Zinberg, J, Woods, SW, Shenton, ME, Wannan, CMJ, Nelson, B, Addington, J, Allott, K, Anticevic, A, Arango, C, Baker, JT, Bearden, CE, Billah, T, Bouix, S, Broome, MR, Buccilli, K, Cadenhead, KS, Calkins, ME, Cannon, TD, Cecci, G, Chen, EYH, Cho, KIK, Choi, J, Clark, SR, Coleman, MJ, Conus, P, Corcoran, CM, Cornblatt, BA, Diaz-Caneja, CM, Dwyer, D, Ebdrup, BH, Ellman, LM, Fusar-Poli, P, Galindo, L, Gaspar, PA, Gerber, C, Glenthoj, LB, Glynn, R, Harms, MP, Horton, LE, Kahn, RS, Kambeitz, J, Kambeitz-Ilankovic, L, Kane, JM, Kapur, T, Keshavan, MS, Kim, S-W, Koutsouleris, N, Kubicki, M, Kwon, JS, Langbein, K, Lewandowski, KE, Light, GA, Mamah, D, Marcy, PJ, Mathalon, DH, McGorry, PD, Mittal, VA, Nordentoft, M, Nunez, A, Pasternak, O, Pearlson, GD, Perez, J, Perkins, DO, Powers, AR, Roalf, DR, Sabb, FW, Schiffman, J, Shah, JL, Smesny, S, Spark, J, Stone, WS, Strauss, GP, Tamayo, Z, Torous, J, Upthegrove, R, Vangel, M, Verma, S, Wang, J, Winter-van Rossum, I, Wolf, DH, Wolff, P, Wood, SJ, Yung, AR, Agurto, C, Alvarez-Jimenez, M, Amminger, P, Armando, M, Asgari-Targhi, A, Cahill, J, Carrion, RE, Castro, E, Cetin-Karayumak, S, Chakravarty, MM, Cho, YT, Cotter, D, D'Alfonso, S, Ennis, M, Fadnavis, S, Fonteneau, C, Gao, C, Gupta, T, Gur, RE, Gur, RC, Hamilton, HK, Hoftman, GD, Jacobs, GR, Jarcho, J, Ji, JL, Kohler, CG, Lalousis, PA, Lavoie, S, Lepage, M, Liebenthal, E, Mervis, J, Murty, V, Nicholas, SC, Ning, L, Penzel, N, Poldrack, R, Polosecki, P, Pratt, DN, Rabin, R, Eichi, HR, Rathi, Y, Reichenberg, A, Reinen, J, Rogers, J, Ruiz-Yu, B, Scott, I, Seitz-Holland, J, Srihari, VH, Srivastava, A, Thompson, A, Turetsky, BI, Walsh, BC, Whitford, T, Wigman, JTW, Yao, B, Yuen, HP, Ahmed, U, Byun, AJS, Chung, Y, Do, K, Hendricks, L, Huynh, K, Jeffries, C, Lane, E, Langholm, C, Lin, E, Mantua, V, Santorelli, G, Ruparel, K, Zoupou, E, Adasme, T, Addamo, L, Adery, L, Ali, M, Auther, A, Aversa, S, Baek, S-H, Bates, K, Bathery, A, Bayer, JMM, Beedham, R, Bilgrami, Z, Birch, S, Bonoldi, I, Borders, O, Borgatti, R, Brown, L, Bruna, A, Carrington, H, Castillo-Passi, RI, Chen, J, Cheng, N, Ching, AE, Clifford, C, Colton, B-L, Contreras, P, Corral, S, Damiani, S, Done, M, Estrade, A, Etuka, BA, Formica, M, Furlan, R, Geljic, M, Germano, C, Getachew, R, Goncalves, M, Haidar, A, Hartmann, J, Jo, A, John, O, Kerins, S, Kerr, M, Kesselring, I, Kim, H, Kim, N, Kinney, K, Krcmar, M, Kotler, E, Lafanechere, M, Lee, C, Llerena, J, Markiewicz, C, Matnejl, P, Maturana, A, Mavambu, A, Mayol-Troncoso, R, McDonnell, A, McGowan, A, McLaughlin, D, McIlhenny, R, McQueen, B, Mebrahtu, Y, Mensi, M, Hui, CLM, Suen, YN, Wong, SMY, Morrell, N, Omar, M, Partridge, A, Phassouliotis, C, Pichiecchio, A, Politi, P, Porter, C, Provenzani, U, Prunier, N, Raj, J, Ray, S, Rayner, V, Reyes, M, Reynolds, K, Rush, S, Salinas, C, Shetty, J, Snowball, C, Tod, S, Turra-Farina, G, Valle, D, Veale, S, Whitson, S, Wickham, A, Youn, S, Zamorano, F, Zavaglia, E, Zinberg, J, Woods, SW, and Shenton, ME

Abstract

This article describes the rationale, aims, and methodology of the Accelerating Medicines Partnership® Schizophrenia (AMP® SCZ). This is the largest international collaboration to date that will develop algorithms to predict trajectories and outcomes of individuals at clinical high risk (CHR) for psychosis and to advance the development and use of novel pharmacological interventions for CHR individuals. We present a description of the participating research networks and the data processing analysis and coordination center, their processes for data harmonization across 43 sites from 13 participating countries (recruitment across North America, Australia, Europe, Asia, and South America), data flow and quality assessment processes, data analyses, and the transfer of data to the National Institute of Mental Health (NIMH) Data Archive (NDA) for use by the research community. In an expected sample of approximately 2000 CHR individuals and 640 matched healthy controls, AMP SCZ will collect clinical, environmental, and cognitive data along with multimodal biomarkers, including neuroimaging, electrophysiology, fluid biospecimens, speech and facial expression samples, novel measures derived from digital health technologies including smartphone-based daily surveys, and passive sensing as well as actigraphy. The study will investigate a range of clinical outcomes over a 2-year period, including transition to psychosis, remission or persistence of CHR status, attenuated positive symptoms, persistent negative symptoms, mood and anxiety symptoms, and psychosocial functioning. The global reach of AMP SCZ and its harmonized innovative methods promise to catalyze the development of new treatments to address critical unmet clinical and public health needs in CHR individuals.

Published
2024

5. Microphysics and dynamics of the Gamma-Ray Burst 121024A

Author

Varela, K., van Eerten, H., Greiner, J., Schady, P., Elliott, J., Sudilovsky, V., Krühler, T., van der Horst, A. J., Bolmer, J., Knust, F., Agurto, C., Azagra, F., Belloche, A., Bertoldi, F., De Breuck, C., Delvaux, C., Filgas, R., Graham, J., Guelbenzu, A. Nicuesa, Kann, D. A., Klose, S., Menten, K. M., Rau, A., Rossi, A., Schmidl, S., Schuller, F., Schweyer, T., Tanga, M ., Weiss, A., Wiseman, P., and Wyrowski, F.

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

Aims. The aim of the study is to constrain the physics of gamma-ray bursts (GRBs) by analysing the multi-wavelength afterglow data set of GRB 121024A that covers the full range from radio to X-rays. Methods. Using multi-epoch broad-band observations of the GRB 121024A afterglow, we measured the three characteristic break frequencies of the synchrotron spectrum. We used six epochs of combined XRT and GROND data to constrain the temporal slopes, the dust extinction, the X-ray absorption, and the spectral slope with high accuracy. Two more epochs of combined data from XRT, GROND, APEX, CARMA, and EVLA were used to set constraints on the break frequencies and therefore on the micro-physical and dynamical parameters. Results. The XRT and GROND light curves show a simultaneous and achromatic break at around 49 ks. As a result, the crossing of the synchrotron cooling break is no suitable explanation for the break in the light curve. The multi wavelength data allow us to test two plausible scenarios explaining the break: a jet break, and the end of energy injection. The jet-break scenario requires a hard electron spectrum, a very low cooling break frequency, and a non-spreading jet. The energy injection avoids these problems, but requires $\epsilon_e > 1 (k = 2)$, spherical outflow, and $\epsilon_B < 10^{-9}$. Conclusions. In light of the extreme microphysical parameters required by the energy-injection model, we favour a jet-break scenario where $\nu_m < \nu_{sa}$ to explain the observations. This scenario gives physically meaningful microphysical parameters, and it also naturally explains the reported detection of linear and circular polarisation., Comment: Final accepted version

Published
2015
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7. Hydrodynamics of a channel occupied by the aquaculture industry in southern Chile: implications for connectivity between farms

Author

Sobarzo, M, Bravo, L, Iturra, C, Troncoso, A, Riquelme, R, Campos, P, and Agurto, C

Subjects
Aquaculture. Fisheries. Angling, SH1-691, Ecology, QH540-549.5
Abstract

Residual circulation from nonlinear interaction of the tidal currents with topography in channels, fjords and bays can be important to represent the distance traveled by suspended materials in the water column (e.g. pathogens). Here the role of the semidiurnal tidal excursion was compared with residual currents, during autumn 2011, to evaluate the connectivity among aquaculture production centers in Caucahue Channel (Chiloe Island, southern Chile), which has been widely occupied by the aquaculture industry. During 2015, around 30000 t of 3 different species of salmon were harvested in this channel, representing 3.7% of the national production. Along- and cross-channel tidal currents explained around 80 and 40-60% of the total variance, respectively. Thus, the major residual circulation came from the cross-channel component (40-60% of the total variance) caused by tidal asymmetry. We hypothesized that this asymmetry is related to the nonlinear interaction of the oscillatory flow with the Quemchi constriction. The residual advective distances (Ladv) were compared with tidal excursion (Lexc) and biological diffusivity (Ldiff) scales, considering the distances between centers (Lint), the size of the centers (Lcen) and the length of the south arm of the Cauchaue Channel (L = 11 km). For 3 d time scales, the Ladv/Lexc ratio fluctuated between 1.3 and 8, approximately, implying that, although the advective scale is greater, the tidal flow is still intense enough to favor the retention of pathogens. For larger time scales that consider longer-lived pathogens (e.g. greater than 15 d), this ratio grows 1 order of magnitude. In this scenario and in the event of an outbreak within the channel, pathogens could be exported.

Published
2018
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8. Crowdsourcing digital health measures to predict Parkinson’s disease severity: the Parkinson’s Disease Digital Biomarker DREAM Challenge

Author

Sieberts, S.K., Schaff, J., Duda, M., Pataki, B.Á., Sun, M., Snyder, P., Daneault, J.F., Parisi, F., Costante, G., Rubin, U., Banda, P., Chae, Y., Chaibub Neto, E., Dorsey, E.R., Aydın, Z., Chen, A., Elo, L.L., Espino, C., Glaab, E., Goan, E., Golabchi, F.N., Görmez, Y., Jaakkola, M.K., Jonnagaddala, J., Klén, R., Li, D., McDaniel, C., Perrin, D., Perumal, T.M., Rad, N.M., Rainaldi, E., Sapienza, S., Schwab, P., Shokhirev, N., Venäläinen, M.S., Vergara-Diaz, G., Zhang, Y., Abrami, A., Adhikary, A., Agurto, C., Bhalla, S., Bilgin, H., Caggiano, V., Cheng, J., Deng, E., Gan, Q., Girsa, R., Han, Z., Heisig, S., Huang, K., Jahandideh, S., Kopp, W., Kurz, C.F., Lichtner, G., Norel, R., Raghava, G.P.S., Sethi, T., Shawen, N., Tripathi, V., Tsai, M., Wang, T., Wu, Y., Zhang, J., Zhang, X., Wang, Y., Guan, Y., Brunner, D., Bonato, P., Mangravite, L.M., Omberg, L., AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü, Aydin, Zafer, Fonds National de la Recherche - FnR [sponsor], and Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group) [research center]

Subjects
Movement disorders, Parkinson's disease, Biotechnologie [F06] [Sciences du vivant], Neurology [D14] [Human health sciences], Medicine (miscellaneous), Disease, Multidisciplinaire, généralités & autres [F99] [Sciences du vivant], 0302 clinical medicine, Health Information Management, Evaluation methods, Biotechnology [F06] [Life sciences], Multidisciplinary, general & others [D99] [Human health sciences], 0303 health sciences, Outcome measures, Computer Science Applications, machine learning, smart sensors, bradykinesia, Biomarker (medicine), Technology Platforms, medicine.symptom, medicine.medical_specialty, Multidisciplinaire, généralités & autres [D99] [Sciences de la santé humaine], Computer applications to medicine. Medical informatics, R858-859.7, Health Informatics, Multidisciplinary, general & others [F99] [Life sciences], Digital Biomarker, Crowdsourcing, Article, VALIDATION, Parkinson’s Disease, 03 medical and health sciences, Physical medicine and rehabilitation, Machine learning, medicine, 030304 developmental biology, mobile phone, GENDER-DIFFERENCES, Neurologie [D14] [Sciences de la santé humaine], business.industry, biomarkers, medicine.disease, tremor, Digital health, nervous system diseases, Clinical trial, dyskinesia, Dyskinesia, Cardiovascular and Metabolic Diseases, HYPOTHESIS TESTS, business, Biomarkers, 030217 neurology & neurosurgery
Abstract

Consumer wearables and sensors are a rich source of data about patients’ daily disease and symptom burden, particularly in the case of movement disorders like Parkinson’s disease (PD). However, interpreting these complex data into so-called digital biomarkers requires complicated analytical approaches, and validating these biomarkers requires sufficient data and unbiased evaluation methods. Here we describe the use of crowdsourcing to specifically evaluate and benchmark features derived from accelerometer and gyroscope data in two different datasets to predict the presence of PD and severity of three PD symptoms: tremor, dyskinesia, and bradykinesia. Forty teams from around the world submitted features, and achieved drastically improved predictive performance for PD status (best AUROC = 0.87), as well as tremor- (best AUPR = 0.75), dyskinesia- (best AUPR = 0.48) and bradykinesia-severity (best AUPR = 0.95)., npj Digital Medicine, 4 (1), ISSN:2398-6352

Published
2021

9. The SEDIGISM survey: molecular clouds in the inner Galaxy

Author

Duarte-Cabral, A., Colombo, D., Urquhart, J. S., Ginsburg, A., Russeil, D., Schuller, F., Anderson, L. D., Barnes, P. J., Beltran, M. T., Beuther, H., Bontemps, S., Bronfman, L., Csengeri, T., Dobbs, C. L., Eden, D., Giannetti, A., Kauffmann, J., Mattern, M., Medina, S-N X., Menten, K. M., Lee, M-Y, Pettitt, A. R., Riener, M., Rigby, A. J., Traficante, A., Veena, V. S., Wienen, M., Wyrowski, F., Agurto, C., Azagra, F., Cesaroni, R., Finger, R., Gonzalez, E., Henning, T., Hernandez, A. K., Kainulainen, J., Leurini, S., Lopez, S., Mac-Auliffe, F., Mazumdar, P., Molinari, S., Motte, F., Muller, E., Nguyen-Luong, Q., Parra, R., Perez-Beaupuits, J-P, Montenegro-Montes, F. M., Moore, T. J. T., Ragan, S. E., Sanchez-Monge, A., Sanna, A., Schilke, P., Schisano, E., Schneider, N., Suri, S., Testi, L., Torstensson, K., Venegas, P., Wang, K., Zavagno, A., Duarte-Cabral, A., Colombo, D., Urquhart, J. S., Ginsburg, A., Russeil, D., Schuller, F., Anderson, L. D., Barnes, P. J., Beltran, M. T., Beuther, H., Bontemps, S., Bronfman, L., Csengeri, T., Dobbs, C. L., Eden, D., Giannetti, A., Kauffmann, J., Mattern, M., Medina, S-N X., Menten, K. M., Lee, M-Y, Pettitt, A. R., Riener, M., Rigby, A. J., Traficante, A., Veena, V. S., Wienen, M., Wyrowski, F., Agurto, C., Azagra, F., Cesaroni, R., Finger, R., Gonzalez, E., Henning, T., Hernandez, A. K., Kainulainen, J., Leurini, S., Lopez, S., Mac-Auliffe, F., Mazumdar, P., Molinari, S., Motte, F., Muller, E., Nguyen-Luong, Q., Parra, R., Perez-Beaupuits, J-P, Montenegro-Montes, F. M., Moore, T. J. T., Ragan, S. E., Sanchez-Monge, A., Sanna, A., Schilke, P., Schisano, E., Schneider, N., Suri, S., Testi, L., Torstensson, K., Venegas, P., Wang, K., and Zavagno, A.

Abstract

We use the (CO)-C-13(2-1) emission from the SEDIGISM (Structure, Excitation, and Dynamics of the Inner Galactic InterStellar Medium) high-resolution spectral-line survey of the inner Galaxy, to extract the molecular cloud population with a large dynamic range in spatial scales, using the Spectral Clustering for Interstellar Molecular Emission Segmentation (SCIMES) algorithm. This work compiles a cloud catalogue with a total of 10 663 molecular clouds, 10 300 of which we were able to assign distances and compute physical properties. We study some of the global properties of clouds using a science sample, consisting of 6664 well-resolved sources and for which the distance estimates are reliable. In particular, we compare the scaling relations retrieved from SEDIGISM to those of other surveys, and we explore the properties of clouds with and without high-mass star formation. Our results suggest that there is no single global property of a cloud that determines its ability to form massive stars, although we find combined trends of increasing mass, size, surface density, and velocity dispersion for the sub-sample of clouds with ongoing high-mass star formation. We then isolate the most extreme clouds in the SEDIGISM sample (i.e. clouds in the tails of the distributions) to look at their overall Galactic distribution, in search for hints of environmental effects. We find that, for most properties, the Galactic distribution of the most extreme clouds is only marginally different to that of the global cloud population. The Galactic distribution of the largest clouds, the turbulent clouds and the high-mass star-forming clouds are those that deviate most significantly from the global cloud population. We also find that the least dynamically active clouds (with low velocity dispersion or low virial parameter) are situated further afield, mostly in the least populated areas. However, we suspect that part of these trends may be affected by some observational biases (such as comp

Published
2021

10. The SEDIGISM survey: First Data Release and overview of the Galactic structure

Author

Schuller, F., Urquhart, J. S., Csengeri, T., Colombo, D., Duarte-Cabral, A., Mattern, M., Ginsburg, A., Pettitt, A. R., Wyrowski, F., Anderson, L., Azagra, F., Barnes, P., Beltran, M., Beuther, H., Billington, S., Bronfman, L., Cesaroni, R., Dobbs, C., Eden, D., Lee, M-Y, Medina, S-N X., Menten, K. M., Moore, T., Montenegro-Montes, F. M., Ragan, S., Rigby, A., Riener, M., Russeil, D., Schisano, E., Sanchez-Monge, A., Traficante, A., Zavagno, A., Agurto, C., Bontemps, S., Finger, R., Giannetti, A., Gonzalez, E., Hernandez, A. K., Henning, T., Kainulainen, J., Kauffmann, J., Leurini, S., Lopez, S., Mac-Auliffe, F., Mazumdar, P., Molinari, S., Motte, F., Muller, E., Nguyen-Luong, Q., Parra, R., Perez-Beaupuits, J-P, Schilke, P., Schneider, N., Suri, S., Testi, L., Torstensson, K., Veena, V. S., Venegas, P., Wang, K., Wienen, M., Schuller, F., Urquhart, J. S., Csengeri, T., Colombo, D., Duarte-Cabral, A., Mattern, M., Ginsburg, A., Pettitt, A. R., Wyrowski, F., Anderson, L., Azagra, F., Barnes, P., Beltran, M., Beuther, H., Billington, S., Bronfman, L., Cesaroni, R., Dobbs, C., Eden, D., Lee, M-Y, Medina, S-N X., Menten, K. M., Moore, T., Montenegro-Montes, F. M., Ragan, S., Rigby, A., Riener, M., Russeil, D., Schisano, E., Sanchez-Monge, A., Traficante, A., Zavagno, A., Agurto, C., Bontemps, S., Finger, R., Giannetti, A., Gonzalez, E., Hernandez, A. K., Henning, T., Kainulainen, J., Kauffmann, J., Leurini, S., Lopez, S., Mac-Auliffe, F., Mazumdar, P., Molinari, S., Motte, F., Muller, E., Nguyen-Luong, Q., Parra, R., Perez-Beaupuits, J-P, Schilke, P., Schneider, N., Suri, S., Testi, L., Torstensson, K., Veena, V. S., Venegas, P., Wang, K., and Wienen, M.

Abstract

The SEDIGISM (Structure, Excitation and Dynamics of the Inner Galactic InterstellarMedium) survey used the APEX telescope to map 84 deg(2) of the Galactic plane between l = -60 degrees and +31 degrees in several molecular transitions, including (CO)-C-13(2 - 1) and (CO)-O-18(2 - 1), thus probing the moderately dense (similar to 10(3) cm(-3)) component of the interstellar medium. With an angular resolution of 30 arcsec and a typical 1 sigma sensitivity of 0.8-1.0K at 0.25 km s(-1) velocity resolution, it gives access to a wide range of structures, from individual star-forming clumps to giant molecular clouds and complexes. The coverage includes a good fraction of the first and fourth Galactic quadrants, allowing us to constrain the large-scale distribution of cold molecular gas in the inner Galaxy. In this paper, we provide an updated overview of the full survey and the data reduction procedures used. We also assess the quality of these data and describe the data products that are being made publicly available as part of this First Data Release (DR1). We present integrated maps and position-velocity maps of the molecular gas and use these to investigate the correlation between the molecular gas and the large-scale structural features of the Milky Way such as the spiral arms, Galactic bar and Galactic Centre. We find that approximately 60 per cent of the molecular gas is associated with the spiral arms and these appear as strong intensity peaks in the derived Galactocentric distribution. We also find strong peaks in intensity at specific longitudes that correspond to the Galactic Centre and well-known star-forming complexes, revealing that the 13CO emission is concentrated in a small number of complexes rather than evenly distributed along spiral arms.

Published
2021

11. Multiscale AM-FM methods for diabetic retinopathy lesion detection

Author

Agurto, C., Murray, V., Barriga, E., Murillo, S., Pattichis, M., Davis, H., Russell, S., Abramoff, M., and Soliz, P.

Subjects
Image processing -- Analysis, Data compression -- Usage, Diabetic retinopathy -- Diagnosis, Frequency modulation -- Methods, Business, Electronics, Electronics and electrical industries, Health care industry
Published
2010

12. Detection of acute 3,4-methylenedioxymethamphetamine (MDMA) effects across protocols using automated natural language processing

Author

Agurto, C, Cecchi, GA, Norel, R, Ostrand, R, Kirkpatrick, M, Baggott, MJ, Wardle, MC, de Wit, H, Bedi, G, Agurto, C, Cecchi, GA, Norel, R, Ostrand, R, Kirkpatrick, M, Baggott, MJ, Wardle, MC, de Wit, H, and Bedi, G

Abstract

The detection of changes in mental states such as those caused by psychoactive drugs relies on clinical assessments that are inherently subjective. Automated speech analysis may represent a novel method to detect objective markers, which could help improve the characterization of these mental states. In this study, we employed computer-extracted speech features from multiple domains (acoustic, semantic, and psycholinguistic) to assess mental states after controlled administration of 3,4-methylenedioxymethamphetamine (MDMA) and intranasal oxytocin. The training/validation set comprised within-participants data from 31 healthy adults who, over four sessions, were administered MDMA (0.75, 1.5 mg/kg), oxytocin (20 IU), and placebo in randomized, double-blind fashion. Participants completed two 5-min speech tasks during peak drug effects. Analyses included group-level comparisons of drug conditions and estimation of classification at the individual level within this dataset and on two independent datasets. Promising classification results were obtained to detect drug conditions, achieving cross-validated accuracies of up to 87% in training/validation and 92% in the independent datasets, suggesting that the detected patterns of speech variability are associated with drug consumption. Specifically, we found that oxytocin seems to be mostly driven by changes in emotion and prosody, which are mainly captured by acoustic features. In contrast, mental states driven by MDMA consumption appear to manifest in multiple domains of speech. Furthermore, we find that the experimental task has an effect on the speech response within these mental states, which can be attributed to presence or absence of an interaction with another individual. These results represent a proof-of-concept application of the potential of speech to provide an objective measurement of mental states elicited during intoxication.

Published
2020

13. The SEDIGISM survey: molecular clouds in the inner Galaxy

Author

Duarte-Cabral, A, primary, Colombo, D, additional, Urquhart, J S, additional, Ginsburg, A, additional, Russeil, D, additional, Schuller, F, additional, Anderson, L D, additional, Barnes, P J, additional, Beltrán, M T, additional, Beuther, H, additional, Bontemps, S, additional, Bronfman, L, additional, Csengeri, T, additional, Dobbs, C L, additional, Eden, D, additional, Giannetti, A, additional, Kauffmann, J, additional, Mattern, M, additional, Medina, S-N X, additional, Menten, K M, additional, Lee, M-Y, additional, Pettitt, A R, additional, Riener, M, additional, Rigby, A J, additional, Traficante, A, additional, Veena, V S, additional, Wienen, M, additional, Wyrowski, F, additional, Agurto, C, additional, Azagra, F, additional, Cesaroni, R, additional, Finger, R, additional, Gonzalez, E, additional, Henning, T, additional, Hernandez, A K, additional, Kainulainen, J, additional, Leurini, S, additional, Lopez, S, additional, Mac-Auliffe, F, additional, Mazumdar, P, additional, Molinari, S, additional, Motte, F, additional, Muller, E, additional, Nguyen-Luong, Q, additional, Parra, R, additional, Perez-Beaupuits, J-P, additional, Montenegro-Montes, F M, additional, Moore, T J T, additional, Ragan, S E, additional, Sánchez-Monge, A, additional, Sanna, A, additional, Schilke, P, additional, Schisano, E, additional, Schneider, N, additional, Suri, S, additional, Testi, L, additional, Torstensson, K, additional, Venegas, P, additional, Wang, K, additional, and Zavagno, A, additional

Published
2020
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14. The SEDIGISM survey: First Data Release and overview of the Galactic structure

Author

Schuller, F, primary, Urquhart, J S, additional, Csengeri, T, additional, Colombo, D, additional, Duarte-Cabral, A, additional, Mattern, M, additional, Ginsburg, A, additional, Pettitt, A R, additional, Wyrowski, F, additional, Anderson, L, additional, Azagra, F, additional, Barnes, P, additional, Beltran, M, additional, Beuther, H, additional, Billington, S, additional, Bronfman, L, additional, Cesaroni, R, additional, Dobbs, C, additional, Eden, D, additional, Lee, M-Y, additional, Medina, S-N X, additional, Menten, K M, additional, Moore, T, additional, Montenegro-Montes, F M, additional, Ragan, S, additional, Rigby, A, additional, Riener, M, additional, Russeil, D, additional, Schisano, E, additional, Sanchez-Monge, A, additional, Traficante, A, additional, Zavagno, A, additional, Agurto, C, additional, Bontemps, S, additional, Finger, R, additional, Giannetti, A, additional, Gonzalez, E, additional, Hernandez, A K, additional, Henning, T, additional, Kainulainen, J, additional, Kauffmann, J, additional, Leurini, S, additional, Lopez, S, additional, Mac-Auliffe, F, additional, Mazumdar, P, additional, Molinari, S, additional, Motte, F, additional, Muller, E, additional, Nguyen-Luong, Q, additional, Parra, R, additional, Perez-Beaupuits, J-P, additional, Schilke, P, additional, Schneider, N, additional, Suri, S, additional, Testi, L, additional, Torstensson, K, additional, Veena, V S, additional, Venegas, P, additional, Wang, K, additional, and Wienen, M, additional

Published
2020
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17. SEDIGISM: Structure, excitation, and dynamics of the inner Galactic interstellar medium

Author

Schuller, F., primary, Csengeri, T., additional, Urquhart, J. S., additional, Duarte-Cabral, A., additional, Barnes, P. J., additional, Giannetti, A., additional, Hernandez, A. K., additional, Leurini, S., additional, Mattern, M., additional, Medina, S.-N. X., additional, Agurto, C., additional, Azagra, F., additional, Anderson, L. D., additional, Beltrán, M. T., additional, Beuther, H., additional, Bontemps, S., additional, Bronfman, L., additional, Dobbs, C. L., additional, Dumke, M., additional, Finger, R., additional, Ginsburg, A., additional, Gonzalez, E., additional, Henning, T., additional, Kauffmann, J., additional, Mac-Auliffe, F., additional, Menten, K. M., additional, Montenegro-Montes, F. M., additional, Moore, T. J. T., additional, Muller, E., additional, Parra, R., additional, Perez-Beaupuits, J.-P., additional, Pettitt, A., additional, Russeil, D., additional, Sánchez-Monge, Á., additional, Schilke, P., additional, Schisano, E., additional, Suri, S., additional, Testi, L., additional, Torstensson, K., additional, Venegas, P., additional, Wang, K., additional, Wienen, M., additional, Wyrowski, F., additional, and Zavagno, A., additional

Published
2017
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18. Microphysics and dynamics of the gamma-ray burst 121024A

Author

Varela, K., primary, van Eerten, H., additional, Greiner, J., additional, Schady, P., additional, Elliott, J., additional, Sudilovsky, V., additional, Krühler, T., additional, van der Horst, A. J., additional, Bolmer, J., additional, Knust, F., additional, Agurto, C., additional, Azagra, F., additional, Belloche, A., additional, Bertoldi, F., additional, De Breuck, C., additional, Delvaux, C., additional, Filgas, R., additional, Graham, J. F., additional, Kann, D. A., additional, Klose, S., additional, Menten, K. M., additional, Nicuesa Guelbenzu, A., additional, Rau, A., additional, Rossi, A., additional, Schmidl, S., additional, Schuller, F., additional, Schweyer, T., additional, Tanga, M., additional, Weiss, A., additional, Wiseman, P., additional, and Wyrowski, F., additional

Published
2016
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23. Multi-scale AM-FM for lesion phenotyping

Author

Barriga, E.S., Murray, V., Agurto, C., Pattichis, M.S., Russell, S., Abramoff, M.D., Davis, H., and Soliz, P.

Subjects
Geneeskunde, Macular Degeneration, genetic structures, sense organs, AM-FM, eye diseases
Abstract

Age-related macular degeneration (AMD) is the most common cause of visual loss in the United States and is a growing public health problem. The presence and severity of AMD in current epidemiological studies is detected by the grading of color stereoscopic fundus photographs. The purpose of this study was to show that a mathematical technique, amplitude-modulation frequency modulation (AM-FM) can be used to generate multi-scale features for classifying pathological structures, such as drusen, on a retinal image. AM-FM features were calculated for N=120 40times40 regions from 5 retinal images presenting with age-related macular degeneration. The results show that with this technique, drusen can be differenced from normal retinal structures by more than three standard deviations using the AM-FM histograms. In addition, by using different color spaces highly accurate classification of structures of the retina is achieved. These results are the first step in the development of an automated AMD grading system.

Published
2009

29. Five-year outcomes of HAART at a non-governmental treatment center in Lima, Peru

Author

Castillo, N., Agurto, C., Benites, C., and Hidalgo, J.A.

Subjects
Highly active antiretroviral therapy -- Dosage and administration -- Patient outcomes, Non-governmental organizations -- Services, HIV infection -- Prevention -- Drug therapy -- Patient outcomes, Health
Abstract

7‐11 November 2010, Tenth International Congress on Drug Therapy in HIV Infection, Glasgow, UK, Background Ministry of Health in Peru launched an HIV treatment program with the initial support of the Global Fund in 2004. A few months later, our institution, an NGO working [...]

Published
2010
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30. Newly diagnosed HIV patients in Lima, Peru: a comparison of individuals diagnosed through an intervention program versus self‐referred individuals

Author

Hidalgo, Ja, Castillo, N, and Agurto, C

Subjects
Health behavior -- Evaluation, Public health administration -- Evaluation, HIV infection -- Diagnosis -- Care and treatment, Health
Abstract

7‐11 November 2010, Tenth International Congress on Drug Therapy in HIV Infection, Glasgow, UK, Background An extensive intervention program to promote awareness, HIV testing, diagnosis and access to medical care in at‐risk populations was developed by Via Libre between Nov 2007 and Oct 2009 [...]

Published
2010
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38. APEX: the Atacama Pathfinder EXperiment

Author

Güsten, R., primary, Booth, R. S., additional, Cesarsky, C., additional, Menten, K. M., additional, Agurto, C., additional, Anciaux, M., additional, Azagra, F., additional, Belitsky, V., additional, Belloche, A., additional, Bergman, P., additional, De Breuck, C., additional, Comito, C., additional, Dumke, M., additional, Duran, C., additional, Esch, W., additional, Fluxa, J., additional, Greve, A., additional, Hafok, H., additional, Häupl, W., additional, Helldner, L., additional, Henseler, A., additional, Heyminck, S., additional, Johansson, L. E., additional, Kasemann, C., additional, Klein, B., additional, Korn, A., additional, Kreysa, E., additional, Kurz, R., additional, Lapkin, I., additional, Leurini, S., additional, Lis, D., additional, Lundgren, A., additional, Mac-Auliffe, F., additional, Martinez, M., additional, Melnick, J., additional, Morris, D., additional, Muders, D., additional, Nyman, L. A., additional, Olberg, M., additional, Olivares, R., additional, Pantaleev, M., additional, Patel, N., additional, Pausch, K., additional, Philipp, S. D., additional, Philipps, S., additional, Sridharan, T. K., additional, Polehampton, E., additional, Reveret, V., additional, Risacher, C., additional, Roa, M., additional, Sauer, P., additional, Schilke, P., additional, Santana, J., additional, Schneider, G., additional, Sepulveda, J., additional, Siringo, G., additional, Spyromilio, J., additional, Stenvers, K.-H., additional, van der Tak, F., additional, Torres, D., additional, Vanzi, L., additional, Vassilev, V., additional, Weiss, A., additional, Willmeroth, K., additional, Wunsch, A., additional, and Wyrowski, F., additional

Published
2006
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44. Fast vessel segmentation in retinal images using multi-scale enhancement and second-order local entropy

Author

Yu, H., Barriga, S., Agurto, C., Zamora, G., Bauman, W., and Soliz, P.

Abstract

Retinal vasculature is one of the most important anatomical structures in digital retinal photographs. Accurate segmentation of retinal blood vessels is an essential task in automated analysis of retinopathy. This paper presents a new and effective vessel segmentation algorithm that features computational simplicity and fast implementation. This method uses morphological pre-processing to decrease the disturbance of bright structures and lesions before vessel extraction. Next, a vessel probability map is generated by computing the eigenvalues of the second derivatives of Gaussian filtered image at multiple scales. Then, the second order local entropy thresholding is applied to segment the vessel map. Lastly, a rule-based decision step, which measures the geometric shape difference between vessels and lesions is applied to reduce false positives. The algorithm is evaluated on the low-resolution DRIVE and STARE databases and the publicly available high-resolution image database from Friedrich-Alexander University Erlangen-Nuremberg (Germany). The proposed method achieved comparable performance to state of the art unsupervised vessel segmentation methods with a competitive faster speed on the DRIVE and STARE databases. For the high resolution fundus image database, the proposed algorithm outperforms an existing approach both on performance and speed. The efficiency and robustness make the blood vessel segmentation method described here suitable for broad application in automated analysis of retinal images.

Published
2012
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47. GRB 091127: LABOCA/APEX submm observations

Author

Ugarte Postigo, A., Lundgren, A., Carlos De Breuck, Montenegro, F., Agurto, C., Gorosabel, J., Jelinek, M., Castro-Tirado, A. J., Kubanek, P., Covino, S., and Thoene, C. C.

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