Gas flows in the circumgalactic medium around simulated high-redshift galaxies

Monthly Notices of the Royal Astronomical Society Oxford University Press 474:4 (2017) 4279-4301

Authors:

PD Mitchell, J Blaizot, Julien Devriendt, T Kimm, L Michel-Dansac, J Rosdahl, Adrianne Slyz

Abstract:

We analyse the properties of circumgalactic gas around simulated galaxies in the redshift range z ≥ 3, utilizing a new sample of cosmological zoom simulations. These simulations are intended to be representative of the observed samples of Lyman α (Ly α) emitters recently obtained with the multi unit spectroscopic explorer (MUSE) instrument (halo masses ~ 10 10 - 10 11 M⊙). We show that supernova feedback has a significant impact on both the inflowing and outflowing circumgalactic medium (CGM) by driving outflows, reducing diffuse inflow rates, and by increasing the neutral fraction of inflowing gas. By temporally stacking simulation outputs, we find that significant net mass exchange occurs between inflowing and outflowing phases: none of the phases are mass-conserving. In particular, we find that the mass in neutral outflowing hydrogen declines exponentially with radius as gas flows outwards from the halo centre. This is likely caused by a combination of both fountain-like cycling processes and gradual photoionization/collisional ionization of outflowing gas. Our simulations do not predict the presence of fast-moving neutral outflows in the CGM. Neutral outflows instead move with modest radial velocities (~ 50 km s -1 ), and the majority of the kinetic energy is associated with tangential rather than radial motion.

Learning Influential Genes on Cancer Gene Expression Data with Stacked Denoising Autoencoders

Institute of Electrical and Electronics Engineers (IEEE) (2017) 1201-1205

Authors:

Vítor Teixeira, Rui Camacho, Pedro G Ferreira

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

Genome Research Cold Spring Harbor Laboratory 27:11 (2017) 1843-1858

Authors:

Ashis Saha, Yungil Kim, Ariel DH Gewirtz, Brian Jo, Chuan Gao, Ian C McDowell, The GTEx Consortium, Barbara E Engelhardt, Alexis Battle, François Aguet, Kristin G Ardlie, Beryl B Cummings, Ellen T Gelfand, Gad Getz, Kane Hadley, Robert E Handsaker, Katherine H Huang, Seva Kashin, Konrad J Karczewski, Monkol Lek, Xiao Li, Daniel G MacArthur, Jared L Nedzel, Duyen T Nguyen, Michael S Noble, Ayellet V Segrè, Casandra A Trowbridge, Taru Tukiainen, Nathan S Abell, Brunilda Balliu, Ruth Barshir, Omer Basha, Alexis Battle, Gireesh K Bogu, Andrew Brown, Christopher D Brown, Stephane E Castel, Lin S Chen, Colby Chiang, Donald F Conrad, Nancy J Cox, Farhan N Damani, Joe R Davis, Olivier Delaneau, Emmanouil T Dermitzakis, Barbara E Engelhardt, Eleazar Eskin, Pedro G Ferreira, Laure Frésard, Eric R Gamazon, Diego Garrido-Martín, Ariel DH Gewirtz, Genna Gliner, Michael J Gloudemans, Roderic Guigo, Ira M Hall, Buhm Han, Yuan He, Farhad Hormozdiari, Cedric Howald, Hae Kyung Im, Brian Jo, Eun Yong Kang, Yungil Kim, Sarah Kim-Hellmuth, Tuuli Lappalainen, Li, Xin Li, Boxiang Liu, Serghei Mangul, Mark I McCarthy, Ian C McDowell, Pejman Mohammadi, Jean Monlong, Stephen B Montgomery, Manuel Muñoz-Aguirre, Anne W Ndungu, Dan L Nicolae, Andrew B Nobel, Meritxell Oliva, Halit Ongen, John J Palowitch, Nikolaos Panousis, Panagiotis Papasaikas, YoSon Park, Princy Parsana, Anthony J Payne, Christine B Peterson, Jie Quan, Ferran Reverter, Chiara Sabatti, Ashis Saha, Michael Sammeth, Alexandra J Scott, Andrey A Shabalin, Reza Sodaei, Matthew Stephens, Barbara E Stranger, Benjamin J Strober, Jae Hoon Sul, Emily K Tsang, Sarah Urbut, Martijn van de Bunt, Gao Wang, Xiaoquan Wen, Fred A Wright, Hualin S Xi, Esti Yeger-Lotem, Zachary Zappala, Judith B Zaugg, Yi-Hui Zhou, Joshua M Akey, Daniel Bates, Joanne Chan, Lin S Chen, Melina Claussnitzer, Kathryn Demanelis, Morgan Diegel, Jennifer A Doherty, Andrew P Feinberg, Marian S Fernando, Jessica Halow, Kasper D Hansen, Eric Haugen, Peter F Hickey, Lei Hou, Farzana Jasmine, Ruiqi Jian, Lihua Jiang, Audra Johnson, Rajinder Kaul, Manolis Kellis, Muhammad G Kibriya, Kristen Lee, Jin Billy Li, Qin Li, Xiao Li, Jessica Lin, Shin Lin, Sandra Linder, Caroline Linke, Yaping Liu, Matthew T Maurano, Benoit Molinie, Stephen B Montgomery, Jemma Nelson, Fidencio J Neri, Meritxell Oliva, Yongjin Park, Brandon L Pierce, Nicola J Rinaldi, Lindsay F Rizzardi, Richard Sandstrom, Andrew Skol, Kevin S Smith, Michael P Snyder, John Stamatoyannopoulos, Barbara E Stranger, Hua Tang, Emily K Tsang, Li Wang, Meng Wang, Nicholas Van Wittenberghe, Fan Wu, Rui Zhang, Concepcion R Nierras, Philip A Branton, Latarsha J Carithers, Ping Guan, Helen M Moore, Abhi Rao, Jimmie B Vaught, Sarah E Gould, Nicole C Lockart, Casey Martin, Jeffery P Struewing, Simona Volpi, Anjene M Addington, Susan E Koester, A Roger Little, Lori E Brigham, Richard Hasz, Marcus Hunter, Christopher Johns, Mark Johnson, Gene Kopen, William F Leinweber, John T Lonsdale, Alisa McDonald, Bernadette Mestichelli, Kevin Myer, Brian Roe, Michael Salvatore, Saboor Shad, Jeffrey A Thomas, Gary Walters, Michael Washington, Joseph Wheeler, Jason Bridge, Barbara A Foster, Bryan M Gillard, Ellen Karasik, Rachna Kumar, Mark Miklos, Michael T Moser, Scott D Jewell, Robert G Montroy, Daniel C Rohrer, Dana R Valley, David A Davis, Deborah C Mash, Anita H Undale, Anna M Smith, David E Tabor, Nancy V Roche, Jeffrey A McLean, Negin Vatanian, Karna L Robinson, Leslie Sobin, Mary E Barcus, Kimberly M Valentino, Liqun Qi, Steven Hunter, Pushpa Hariharan, Shilpi Singh, Ki Sung Um, Takunda Matose, Maria M Tomaszewski, Laura K Barker, Maghboeba Mosavel, Laura A Siminoff, Heather M Traino, Paul Flicek, Thomas Juettemann, Magali Ruffier, Dan Sheppard, Kieron Taylor, Stephen J Trevanion, Daniel R Zerbino, Brian Craft, Mary Goldman, Maximilian Haeussler, W James Kent, Christopher M Lee, Benedict Paten, Kate R Rosenbloom, John Vivian, Jingchun Zhu

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

Genome Research Cold Spring Harbor Laboratory 27:11 (2017) 1859-1871

Authors:

Fan Yang, Jiebiao Wang, The GTEx Consortium, Brandon L Pierce, Lin S Chen, François Aguet, Kristin G Ardlie, Beryl B Cummings, Ellen T Gelfand, Gad Getz, Kane Hadley, Robert E Handsaker, Katherine H Huang, Seva Kashin, Konrad J Karczewski, Monkol Lek, Xiao Li, Daniel G MacArthur, Jared L Nedzel, Duyen T Nguyen, Michael S Noble, Ayellet V Segrè, Casandra A Trowbridge, Taru Tukiainen, Nathan S Abell, Brunilda Balliu, Ruth Barshir, Omer Basha, Alexis Battle, Gireesh K Bogu, Andrew Brown, Christopher D Brown, Stephane E Castel, Lin S Chen, Colby Chiang, Donald F Conrad, Nancy J Cox, Farhan N Damani, Joe R Davis, Olivier Delaneau, Emmanouil T Dermitzakis, Barbara E Engelhardt, Eleazar Eskin, Pedro G Ferreira, Laure Frésard, Eric R Gamazon, Diego Garrido-Martín, Ariel DH Gewirtz, Genna Gliner, Michael J Gloudemans, Roderic Guigo, Ira M Hall, Buhm Han, Yuan He, Farhad Hormozdiari, Cedric Howald, Hae Kyung Im, Brian Jo, Eun Yong Kang, Yungil Kim, Sarah Kim-Hellmuth, Tuuli Lappalainen, Li, Xin Li, Boxiang Liu, Serghei Mangul, Mark I McCarthy, Ian C McDowell, Pejman Mohammadi, Jean Monlong, Stephen B Montgomery, Manuel Muñoz-Aguirre, Anne W Ndungu, Dan L Nicolae, Andrew B Nobel, Meritxell Oliva, Halit Ongen, John J Palowitch, Nikolaos Panousis, Panagiotis Papasaikas, YoSon Park, Princy Parsana, Anthony J Payne, Christine B Peterson, Jie Quan, Ferran Reverter, Chiara Sabatti, Ashis Saha, Michael Sammeth, Alexandra J Scott, Andrey A Shabalin, Reza Sodaei, Matthew Stephens, Barbara E Stranger, Benjamin J Strober, Jae Hoon Sul, Emily K Tsang, Sarah Urbut, Martijn van de Bunt, Gao Wang, Xiaoquan Wen, Fred A Wright, Hualin S Xi, Esti Yeger-Lotem, Zachary Zappala, Judith B Zaugg, Yi-Hui Zhou, Joshua M Akey, Daniel Bates, Joanne Chan, Lin S Chen, Melina Claussnitzer, Kathryn Demanelis, Morgan Diegel, Jennifer A Doherty, Andrew P Feinberg, Marian S Fernando, Jessica Halow, Kasper D Hansen, Eric Haugen, Peter F Hickey, Lei Hou, Farzana Jasmine, Ruiqi Jian, Lihua Jiang, Audra Johnson, Rajinder Kaul, Manolis Kellis, Muhammad G Kibriya, Kristen Lee, Jin Billy Li, Qin Li, Xiao Li, Jessica Lin, Shin Lin, Sandra Linder, Caroline Linke, Yaping Liu, Matthew T Maurano, Benoit Molinie, Stephen B Montgomery, Jemma Nelson, Fidencio J Neri, Meritxell Oliva, Yongjin Park, Brandon L Pierce, Nicola J Rinaldi, Lindsay F Rizzardi, Richard Sandstrom, Andrew Skol, Kevin S Smith, Michael P Snyder, John Stamatoyannopoulos, Barbara E Stranger, Hua Tang, Emily K Tsang, Li Wang, Meng Wang, Nicholas Van Wittenberghe, Fan Wu, Rui Zhang, Concepcion R Nierras, Philip A Branton, Latarsha J Carithers, Ping Guan, Helen M Moore, Abhi Rao, Jimmie B Vaught, Sarah E Gould, Nicole C Lockart, Casey Martin, Jeffery P Struewing, Simona Volpi, Anjene M Addington, Susan E Koester, A Roger Little, Lori E Brigham, Richard Hasz, Marcus Hunter, Christopher Johns, Mark Johnson, Gene Kopen, William F Leinweber, John T Lonsdale, Alisa McDonald, Bernadette Mestichelli, Kevin Myer, Brian Roe, Michael Salvatore, Saboor Shad, Jeffrey A Thomas, Gary Walters, Michael Washington, Joseph Wheeler, Jason Bridge, Barbara A Foster, Bryan M Gillard, Ellen Karasik, Rachna Kumar, Mark Miklos, Michael T Moser, Scott D Jewell, Robert G Montroy, Daniel C Rohrer, Dana R Valley, David A Davis, Deborah C Mash, Anita H Undale, Anna M Smith, David E Tabor, Nancy V Roche, Jeffrey A McLean, Negin Vatanian, Karna L Robinson, Leslie Sobin, Mary E Barcus, Kimberly M Valentino, Liqun Qi, Steven Hunter, Pushpa Hariharan, Shilpi Singh, Ki Sung Um, Takunda Matose, Maria M Tomaszewski, Laura K Barker, Maghboeba Mosavel, Laura A Siminoff, Heather M Traino, Paul Flicek, Thomas Juettemann, Magali Ruffier, Dan Sheppard, Kieron Taylor, Stephen J Trevanion, Daniel R Zerbino, Brian Craft, Mary Goldman, Maximilian Haeussler, W James Kent, Christopher M Lee, Benedict Paten, Kate R Rosenbloom, John Vivian, Jingchun Zhu

KiDS-450 + 2dFLenS: Cosmological parameter constraints from weak gravitational lensing tomography and overlapping redshift-space galaxy clustering

Monthly Notices of the Royal Astronomical Society Oxford University Press 474:4 (2017) 4894-4924

Authors:

Shahab Joudaki, C Blake, A Johnson, A Amon, M Asgari, A Choi, T Erben, K Glazebrook, J Harnois-Déraps, C Heymans, H Hildebrandt, H Hoekstra, D Klaes, K Kuijken, C Lidman, A Mead, Lance Miller, D Parkinson, GB Poole, P Schneider, M Viola, C Wolf

Abstract:

We perform a combined analysis of cosmic shear tomography, galaxy-galaxy lensing tomography, and redshift-space multipole power spectra (monopole and quadrupole) using 450 deg$^2$ of imaging data by the Kilo Degree Survey (KiDS) overlapping with two spectroscopic surveys: the 2-degree Field Lensing Survey (2dFLenS) and the Baryon Oscillation Spectroscopic Survey (BOSS). We restrict the galaxy-galaxy lensing and multipole power spectrum measurements to the overlapping regions with KiDS, and self-consistently compute the full covariance between the different observables using a large suite of $N$-body simulations. We methodically analyze different combinations of the observables, finding that galaxy-galaxy lensing measurements are particularly useful in improving the constraint on the intrinsic alignment amplitude (by 30%, positive at $3.5\sigma$ in the fiducial data analysis), while the multipole power spectra are useful in tightening the constraints along the lensing degeneracy direction (e.g. factor of two stronger matter density constraint in the fiducial analysis). The fully combined constraint on $S_8 \equiv \sigma_8 \sqrt{\Omega_{\rm m}/0.3} = 0.742 \pm 0.035$, which is an improvement by 20% compared to KiDS alone, corresponds to a $2.6\sigma$ discordance with Planck, and is not significantly affected by fitting to a more conservative set of scales. Given the tightening of the parameter space, we are unable to resolve the discordance with an extended cosmology that is simultaneously favored in a model selection sense, including the sum of neutrino masses, curvature, evolving dark energy, and modified gravity. The complementarity of our observables allows for constraints on modified gravity degrees of freedom that are not simultaneously bounded with either probe alone, and up to a factor of three improvement in the $S_8$ constraint in the extended cosmology compared to KiDS alone.