[{"scopus_import":"1","type":"journal_article","publication":"The Astrophysical Journal","page":"627-631","doi":"10.1086/428645","day":"20","status":"public","publication_status":"published","intvolume":"       623","article_processing_charge":"No","title":"Constraining reionization with the evolution of the luminosity function of Lyα emitting galaxies","publisher":"American Astronomical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","date_updated":"2024-09-25T12:55:58Z","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1086/428645"}],"abstract":[{"text":"At redshifts beyond z>6, as the mean fraction of neutral hydrogen x_HI in the intergalactic medium (IGM) increases, the line flux of Lyman alpha (Lya) emitters can be significantly suppressed, which can result in a decrease in the observed number of emitters at a given Lya flux. However, cosmological HII regions surrounding the Lya emitting galaxies alleviate these effects. We use simple models of the Lya line suppression that incorporate the presence of HII regions to predict the overall effect of the Lya absorption on the Lya luminosity function. We find, in agreement with other recent studies, that unless ionizing sources are unusually strongly clustered, a fully neutral IGM may be inconsistent with the large abundance of confirmed z=6.5 Lya emitters. However, the presence of local HII regions prohibits placing a tight constraint on the mean neutral fraction. We find x_HI < 0.25; the presence of strong winds and/or the clustering of ionizing sources would further weaken this constraint. We conclude that the evolution of the Lya LF is consistent with reionization occurring near this redshift. Finally, we suggest that a measurement of observed Lya line width as a function of the Lya luminosity, in a future, larger sample of Lya emitters, may serve as a robust diagnostic of the neutral fraction in the IGM.","lang":"eng"}],"citation":{"apa":"Haiman, Z., &#38; Cen, R. (2005). Constraining reionization with the evolution of the luminosity function of Lyα emitting galaxies. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1086/428645\">https://doi.org/10.1086/428645</a>","ista":"Haiman Z, Cen R. 2005. Constraining reionization with the evolution of the luminosity function of Lyα emitting galaxies. The Astrophysical Journal. 623(2), 627–631.","mla":"Haiman, Zoltán, and Renyue Cen. “Constraining Reionization with the Evolution of the Luminosity Function of Lyα Emitting Galaxies.” <i>The Astrophysical Journal</i>, vol. 623, no. 2, American Astronomical Society, 2005, pp. 627–31, doi:<a href=\"https://doi.org/10.1086/428645\">10.1086/428645</a>.","chicago":"Haiman, Zoltán, and Renyue Cen. “Constraining Reionization with the Evolution of the Luminosity Function of Lyα Emitting Galaxies.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2005. <a href=\"https://doi.org/10.1086/428645\">https://doi.org/10.1086/428645</a>.","short":"Z. Haiman, R. Cen, The Astrophysical Journal 623 (2005) 627–631.","ama":"Haiman Z, Cen R. Constraining reionization with the evolution of the luminosity function of Lyα emitting galaxies. <i>The Astrophysical Journal</i>. 2005;623(2):627-631. doi:<a href=\"https://doi.org/10.1086/428645\">10.1086/428645</a>","ieee":"Z. Haiman and R. Cen, “Constraining reionization with the evolution of the luminosity function of Lyα emitting galaxies,” <i>The Astrophysical Journal</i>, vol. 623, no. 2. American Astronomical Society, pp. 627–631, 2005."},"oa_version":"Published Version","year":"2005","oa":1,"issue":"2","quality_controlled":"1","extern":"1","date_created":"2024-09-06T08:59:08Z","language":[{"iso":"eng"}],"author":[{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán","full_name":"Haiman, Zoltán","last_name":"Haiman"},{"full_name":"Cen, Renyue","first_name":"Renyue","last_name":"Cen"}],"_id":"17715","date_published":"2005-04-20T00:00:00Z","publication_identifier":{"issn":["0004-637X","1538-4357"]},"volume":623},{"month":"07","main_file_link":[{"url":"https://doi.org/10.1086/430696","open_access":"1"}],"citation":{"ieee":"D. S. Spiegel, M. Zamojski, A. Gersch, J. Donovan, and Z. Haiman, “Can we probe the atmospheric composition of an extrasolar planet from its reflection spectrum in a high‐magnification microlensing event?,” <i>The Astrophysical Journal</i>, vol. 628, no. 1. American Astronomical Society, pp. 478–486, 2005.","ama":"Spiegel DS, Zamojski M, Gersch A, Donovan J, Haiman Z. Can we probe the atmospheric composition of an extrasolar planet from its reflection spectrum in a high‐magnification microlensing event? <i>The Astrophysical Journal</i>. 2005;628(1):478-486. doi:<a href=\"https://doi.org/10.1086/430696\">10.1086/430696</a>","short":"D.S. Spiegel, M. Zamojski, A. Gersch, J. Donovan, Z. Haiman, The Astrophysical Journal 628 (2005) 478–486.","ista":"Spiegel DS, Zamojski M, Gersch A, Donovan J, Haiman Z. 2005. Can we probe the atmospheric composition of an extrasolar planet from its reflection spectrum in a high‐magnification microlensing event? The Astrophysical Journal. 628(1), 478–486.","apa":"Spiegel, D. S., Zamojski, M., Gersch, A., Donovan, J., &#38; Haiman, Z. (2005). Can we probe the atmospheric composition of an extrasolar planet from its reflection spectrum in a high‐magnification microlensing event? <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1086/430696\">https://doi.org/10.1086/430696</a>","mla":"Spiegel, David S., et al. “Can We Probe the Atmospheric Composition of an Extrasolar Planet from Its Reflection Spectrum in a High‐magnification Microlensing Event?” <i>The Astrophysical Journal</i>, vol. 628, no. 1, American Astronomical Society, 2005, pp. 478–86, doi:<a href=\"https://doi.org/10.1086/430696\">10.1086/430696</a>.","chicago":"Spiegel, David S., Michel Zamojski, Alan Gersch, Jennifer Donovan, and Zoltán Haiman. “Can We Probe the Atmospheric Composition of an Extrasolar Planet from Its Reflection Spectrum in a High‐magnification Microlensing Event?” <i>The Astrophysical Journal</i>. American Astronomical Society, 2005. <a href=\"https://doi.org/10.1086/430696\">https://doi.org/10.1086/430696</a>."},"abstract":[{"text":"We revisit the possibility of detecting an extrasolar planet around a background star as it crosses the fold caustic of a foreground binary lens. During such an event, the planet's flux can be magnified by a factor of ~100 or more. The detectability of the planet depends strongly on the orientation of its orbit relative to the caustic. If the source star is inside the intercaustic region, detecting the caustic-crossing planet is difficult against the magnified flux of its parent star. In the more favorable configuration, when the star is outside the intercaustic region when the planet crosses the caustic, a close-in Jupiter-like planet around a Sun-like star at a distance of 8 kpc is detectable in 8 minute integrations with a 10 m telescope at maximal signal-to-noise ratio (S/N) ~15 for phase angle ϕ ~ 10°. In this example, we find further that the presence of methane, at its measured abundance in Jupiter, and/or water, sodium, and potassium, at the abundances expected in theoretical atmosphere models of close-in Jupiters, could be inferred from a nondetection of the planet in strong broad absorption bands at 0.6-1.4 μm caused by these compounds, accompanied by a S/N ~ 10 detection in adjacent bands. We conclude that future generations of large telescopes might be able to probe the composition of the atmospheres of distant extrasolar planets.","lang":"eng"}],"oa_version":"Published Version","year":"2005","oa":1,"issue":"1","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2024-09-06T09:05:00Z","extern":"1","_id":"17720","author":[{"last_name":"Spiegel","full_name":"Spiegel, David S.","first_name":"David S."},{"last_name":"Zamojski","full_name":"Zamojski, Michel","first_name":"Michel"},{"first_name":"Alan","full_name":"Gersch, Alan","last_name":"Gersch"},{"last_name":"Donovan","first_name":"Jennifer","full_name":"Donovan, Jennifer"},{"last_name":"Haiman","full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán"}],"date_published":"2005-07-20T00:00:00Z","publication_identifier":{"issn":["0004-637X","1538-4357"]},"volume":628,"scopus_import":"1","type":"journal_article","publication":"The Astrophysical Journal","page":"478-486","doi":"10.1086/430696","status":"public","day":"20","publication_status":"published","intvolume":"       628","article_processing_charge":"No","publisher":"American Astronomical Society","title":"Can we probe the atmospheric composition of an extrasolar planet from its reflection spectrum in a high‐magnification microlensing event?","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2024-09-25T13:51:34Z","article_type":"original"},{"_id":"17731","author":[{"last_name":"Kocsis","full_name":"Kocsis, Bence","first_name":"Bence"},{"full_name":"Haiman, Zoltán","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman"},{"full_name":"Frei, Zsolt","first_name":"Zsolt","last_name":"Frei"}],"publication_identifier":{"issn":["0004-637X","1538-4357"]},"date_published":"2005-04-20T00:00:00Z","volume":623,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1086/427975"}],"month":"04","oa_version":"Published Version","citation":{"short":"B. Kocsis, Z. Haiman, Z. Frei, The Astrophysical Journal 623 (2005) 632–649.","chicago":"Kocsis, Bence, Zoltán Haiman, and Zsolt Frei. “Can Virialization Shocks Be Detected around Galaxy Clusters through the Sunyaev‐Zel’dovich Effect?” <i>The Astrophysical Journal</i>. American Astronomical Society, 2005. <a href=\"https://doi.org/10.1086/427975\">https://doi.org/10.1086/427975</a>.","apa":"Kocsis, B., Haiman, Z., &#38; Frei, Z. (2005). Can virialization shocks be detected around galaxy clusters through the Sunyaev‐Zel’dovich effect? <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1086/427975\">https://doi.org/10.1086/427975</a>","ista":"Kocsis B, Haiman Z, Frei Z. 2005. Can virialization shocks be detected around galaxy clusters through the Sunyaev‐Zel’dovich effect? The Astrophysical Journal. 623(2), 632–649.","mla":"Kocsis, Bence, et al. “Can Virialization Shocks Be Detected around Galaxy Clusters through the Sunyaev‐Zel’dovich Effect?” <i>The Astrophysical Journal</i>, vol. 623, no. 2, American Astronomical Society, 2005, pp. 632–49, doi:<a href=\"https://doi.org/10.1086/427975\">10.1086/427975</a>.","ieee":"B. Kocsis, Z. Haiman, and Z. Frei, “Can virialization shocks be detected around galaxy clusters through the Sunyaev‐Zel’dovich effect?,” <i>The Astrophysical Journal</i>, vol. 623, no. 2. American Astronomical Society, pp. 632–649, 2005.","ama":"Kocsis B, Haiman Z, Frei Z. Can virialization shocks be detected around galaxy clusters through the Sunyaev‐Zel’dovich effect? <i>The Astrophysical Journal</i>. 2005;623(2):632-649. doi:<a href=\"https://doi.org/10.1086/427975\">10.1086/427975</a>"},"abstract":[{"lang":"eng","text":"In cosmological structure formation models, massive non-linear objects in the process of formation, such as galaxy clusters, are surrounded by large-scale shocks at or around the expected virial radius. Direct observational evidence for such virial shocks is currently lacking, but we show here that their presence can be inferred from future, high resolution, high-sensitivity observations of the Sunyaev-Zel'dovich (SZ) effect in galaxy clusters. We study the detectability of virial shocks in mock SZ maps, using simple models of cluster structure (gas density and temperature distributions) and noise (background and foreground galaxy clusters projected along the line of sight, as well as the cosmic microwave background anisotropies). We find that at an angular resolution of 2'' and sensitivity of 10 micro K, expected to be reached at ~ 100 GHz frequencies in a ~ 20 hr integration with the forthcoming ALMA instrument, virial shocks associated with massive M ~ 10^15 M_Sun clusters will stand out from the noise, and can be detected at high significance. More generally, our results imply that the projected SZ surface brightness profile in future, high-resolution experiments will provide sensitive constraints on the density profile of cluster gas."}],"issue":"2","year":"2005","oa":1,"extern":"1","language":[{"iso":"eng"}],"date_created":"2024-09-06T09:16:44Z","quality_controlled":"1","article_processing_charge":"No","intvolume":"       623","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Can virialization shocks be detected around galaxy clusters through the Sunyaev‐Zel’dovich effect?","publisher":"American Astronomical Society","article_type":"original","date_updated":"2024-09-26T07:37:23Z","type":"journal_article","scopus_import":"1","page":"632-649","publication":"The Astrophysical Journal","doi":"10.1086/427975","status":"public","day":"20","publication_status":"published"},{"author":[{"full_name":"Mesinger, Andrei","first_name":"Andrei","last_name":"Mesinger"},{"first_name":"Rosalba","full_name":"Perna, Rosalba","last_name":"Perna"},{"full_name":"Haiman, Zoltán","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman"}],"_id":"17737","volume":623,"date_published":"2005-04-10T00:00:00Z","publication_identifier":{"issn":["0004-637X","1538-4357"]},"abstract":[{"text":"Cosmological models that include suppression of the power spectrum of density fluctuations on small scales exhibit an exponential reduction of high-redshift, non-linear structures, including a reduction in the rate of gamma ray bursts (GRBs). Here we quantify the constraints that the detection of distant GRBs would place on structure formation models with reduced small-scale power. We compute the number of GRBs that could be detectable by the Swift satellite at high redshifts (z > 6), assuming that the GRBs trace the cosmic star formation history, which itself traces the formation of non-linear structures. We calibrate simple models of the intrinsic luminosity function of the bursts to the number and flux distribution of GRBs observed by the Burst And Transient Source Experiment (BATSE). We find that a discovery of high-z GRBs would imply strong constraints on models with reduced small-scale power. For example, a single GRB at z > 10, or 10 GRBs at z > 5, discovered by Swift during its scheduled two-year mission, would rule out an exponential suppression of the power spectrum on scales below R_c=0.09 Mpc (exemplified by warm dark matter models with a particle mass of m_x=2 keV). Models with a less sharp suppression of small-scale power, such as those with a red tilt or a running scalar index, n_s, are more difficult to constrain, because they are more degenerate with an increase in the power spectrum normalization, sigma_8, and with models in which star-formation is allowed in low-mass minihalos. We find that a tilt of \\delta n_s ~ 0.1 is difficult to detect; however, an observed rate of 1 GRB/yr at z > 12 would yield an upper limit on the running of the spectral index, alpha = d(n_s)/d(ln k) > -0.05.","lang":"eng"}],"citation":{"mla":"Mesinger, Andrei, et al. “Constraints on the Small‐scale Power Spectrum of Density Fluctuations from High‐redshift Gamma‐ray Bursts.” <i>The Astrophysical Journal</i>, vol. 623, no. 1, American Astronomical Society, 2005, pp. 1–10, doi:<a href=\"https://doi.org/10.1086/428770\">10.1086/428770</a>.","ista":"Mesinger A, Perna R, Haiman Z. 2005. Constraints on the small‐scale power spectrum of density fluctuations from high‐redshift gamma‐ray bursts. The Astrophysical Journal. 623(1), 1–10.","apa":"Mesinger, A., Perna, R., &#38; Haiman, Z. (2005). Constraints on the small‐scale power spectrum of density fluctuations from high‐redshift gamma‐ray bursts. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1086/428770\">https://doi.org/10.1086/428770</a>","chicago":"Mesinger, Andrei, Rosalba Perna, and Zoltán Haiman. “Constraints on the Small‐scale Power Spectrum of Density Fluctuations from High‐redshift Gamma‐ray Bursts.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2005. <a href=\"https://doi.org/10.1086/428770\">https://doi.org/10.1086/428770</a>.","short":"A. Mesinger, R. Perna, Z. Haiman, The Astrophysical Journal 623 (2005) 1–10.","ama":"Mesinger A, Perna R, Haiman Z. Constraints on the small‐scale power spectrum of density fluctuations from high‐redshift gamma‐ray bursts. <i>The Astrophysical Journal</i>. 2005;623(1):1-10. doi:<a href=\"https://doi.org/10.1086/428770\">10.1086/428770</a>","ieee":"A. Mesinger, R. Perna, and Z. Haiman, “Constraints on the small‐scale power spectrum of density fluctuations from high‐redshift gamma‐ray bursts,” <i>The Astrophysical Journal</i>, vol. 623, no. 1. American Astronomical Society, pp. 1–10, 2005."},"oa_version":"Published Version","month":"04","main_file_link":[{"url":"https://doi.org/10.1086/428770","open_access":"1"}],"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2024-09-06T09:20:42Z","extern":"1","oa":1,"year":"2005","issue":"1","publisher":"American Astronomical Society","title":"Constraints on the small‐scale power spectrum of density fluctuations from high‐redshift gamma‐ray bursts","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       623","article_processing_charge":"No","article_type":"original","date_updated":"2024-09-26T14:02:13Z","publication":"The Astrophysical Journal","page":"1-10","scopus_import":"1","type":"journal_article","publication_status":"published","status":"public","day":"10","doi":"10.1086/428770"},{"quality_controlled":"1","extern":"1","date_created":"2024-09-06T09:48:59Z","language":[{"iso":"eng"}],"oa":1,"year":"2005","issue":"1","abstract":[{"text":"We explore the possibility of resolving an image of a damped Lyα (DLA) system in absorption against an extended, diffuse, background X-ray source. Typical columns of neutral hydrogen in DLA systems are high enough to block out up to ~30% of the soft X-ray flux at an observed photon energy of 0.5 keV, and we find that ~1% of the area of extended X-ray sources at z ≳ 1 have their 0.5 keV flux reduced by at least 20% because of intervening DLA systems. We discuss the observability of such absorption and find that ≳300 photons per angular resolution element are required in the 0.3-8 keV band for its detection and in order to distinguish it from intrinsic surface brightness fluctuations. For the surface brightness of the currently known high-redshift extended X-ray sources, this requires an integration time of a few megaseconds on Chandra, if the maps are smoothed spatially to ≈2'' resolution. The exact required integration time depends on the DLA system's column density, metallicity, and, most strongly, its redshift. Current X-ray telescopes are likely to detect DLA systems with N < 10^22 cm^-2 only out to z ≈ 2.3. The availability of DLA systems with a suitably high column density for a silhouette detection is currently poorly known. We suggest that at low redshifts archival data of bright X-ray point sources may be useful in constraining the high-N end of the column density distribution. We briefly discuss an alternative strategy of searching for extended X-ray sources behind known DLA systems. Although with current X-ray telescopes the detections are challenging, they will be within the reach of a routine observation with a next generation X-ray telescope, such as the X-Ray Evolving Universe Spectrometer (XEUS) or Generation-X, and will deliver novel constraints on the nature of protogalaxies.","lang":"eng"}],"citation":{"apa":"Dijkstra, M., Haiman, Z., &#38; Scharf, C. (2005). On detecting the X‐ray silhouette of a damped Lyα system. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1086/428766\">https://doi.org/10.1086/428766</a>","ista":"Dijkstra M, Haiman Z, Scharf C. 2005. On detecting the X‐ray silhouette of a damped Lyα system. The Astrophysical Journal. 624(1), 85–93.","mla":"Dijkstra, Mark, et al. “On Detecting the X‐ray Silhouette of a Damped Lyα System.” <i>The Astrophysical Journal</i>, vol. 624, no. 1, American Astronomical Society, 2005, pp. 85–93, doi:<a href=\"https://doi.org/10.1086/428766\">10.1086/428766</a>.","chicago":"Dijkstra, Mark, Zoltán Haiman, and Caleb Scharf. “On Detecting the X‐ray Silhouette of a Damped Lyα System.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2005. <a href=\"https://doi.org/10.1086/428766\">https://doi.org/10.1086/428766</a>.","short":"M. Dijkstra, Z. Haiman, C. Scharf, The Astrophysical Journal 624 (2005) 85–93.","ama":"Dijkstra M, Haiman Z, Scharf C. On detecting the X‐ray silhouette of a damped Lyα system. <i>The Astrophysical Journal</i>. 2005;624(1):85-93. doi:<a href=\"https://doi.org/10.1086/428766\">10.1086/428766</a>","ieee":"M. Dijkstra, Z. Haiman, and C. Scharf, “On detecting the X‐ray silhouette of a damped Lyα system,” <i>The Astrophysical Journal</i>, vol. 624, no. 1. American Astronomical Society, pp. 85–93, 2005."},"oa_version":"Published Version","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1086/428766"}],"volume":624,"date_published":"2005-05-01T00:00:00Z","publication_identifier":{"issn":["0004-637X","1538-4357"]},"_id":"17761","author":[{"full_name":"Dijkstra, Mark","first_name":"Mark","last_name":"Dijkstra"},{"last_name":"Haiman","full_name":"Haiman, Zoltán","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"},{"last_name":"Scharf","first_name":"Caleb","full_name":"Scharf, Caleb"}],"publication_status":"published","status":"public","day":"01","doi":"10.1086/428766","publication":"The Astrophysical Journal","page":"85-93","scopus_import":"1","type":"journal_article","date_updated":"2024-09-30T08:55:54Z","article_type":"original","title":"On detecting the X‐ray silhouette of a damped Lyα system","publisher":"American Astronomical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       624","article_processing_charge":"No"},{"date_published":"2005-06-20T00:00:00Z","publication_identifier":{"issn":["0004-637X","1538-4357"]},"volume":626,"_id":"17774","author":[{"last_name":"Malhotra","first_name":"S.","full_name":"Malhotra, S."},{"full_name":"Rhoads, J. E.","first_name":"J. E.","last_name":"Rhoads"},{"last_name":"Pirzkal","full_name":"Pirzkal, N.","first_name":"N."},{"full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán","last_name":"Haiman"},{"full_name":"Xu, C.","first_name":"C.","last_name":"Xu"},{"full_name":"Daddi, E.","first_name":"E.","last_name":"Daddi"},{"full_name":"Yan, H.","first_name":"H.","last_name":"Yan"},{"first_name":"L. E.","full_name":"Bergeron, L. E.","last_name":"Bergeron"},{"last_name":"Wang","first_name":"J.","full_name":"Wang, J."},{"full_name":"Ferguson, H. C.","first_name":"H. C.","last_name":"Ferguson"},{"first_name":"C.","full_name":"Gronwall, C.","last_name":"Gronwall"},{"last_name":"Koekemoer","full_name":"Koekemoer, A.","first_name":"A."},{"full_name":"Kuemmel, M.","first_name":"M.","last_name":"Kuemmel"},{"first_name":"L. A.","full_name":"Moustakas, L. A.","last_name":"Moustakas"},{"first_name":"N.","full_name":"Panagia, N.","last_name":"Panagia"},{"full_name":"Pasquali, A.","first_name":"A.","last_name":"Pasquali"},{"full_name":"Stiavelli, M.","first_name":"M.","last_name":"Stiavelli"},{"last_name":"Walsh","full_name":"Walsh, J.","first_name":"J."},{"first_name":"R. A.","full_name":"Windhorst, R. A.","last_name":"Windhorst"},{"last_name":"di Serego Alighieri","full_name":"di Serego Alighieri, S.","first_name":"S."}],"year":"2005","oa":1,"issue":"2","quality_controlled":"1","extern":"1","language":[{"iso":"eng"}],"date_created":"2024-09-06T10:04:19Z","month":"06","main_file_link":[{"url":"https://doi.org/10.1086/430047","open_access":"1"}],"abstract":[{"lang":"eng","text":"We present grism spectra taken with the Advanced Camera for Surveys (ACS) to identify 29 red sources with (i775 - z850) ≥ 0.9 in the Hubble Ultra Deep Field (HUDF). Of these, 23 are found to be galaxies at redshifts between z = 5.4 and 6.7, identified by the break at 1216 Å due to intergalactic medium (IGM) absorption; two are late-type dwarf stars with red colors; and four are galaxies with colors and spectral shapes similar to dust-reddened or old galaxies at redshifts z ≈ 1-2. This constitutes the largest uniform, flux-limited sample of spectroscopically confirmed galaxies at such faint fluxes (z850 ≤ 27.5). Many are also among the most distant spectroscopically confirmed galaxies (at redshifts up to z = 6.7). We find a significant overdensity of galaxies at redshifts z = 5.9 ± 0.2. Nearly two-thirds of the galaxies in our sample (15/23) belong to this peak. Taking into account the selection function and the redshift sensitivity of the survey, we get a conservative overdensity of at least a factor of 2 along the line of sight. The galaxies found in this redshift peak are also localized in the plane of the sky in a nonrandom manner, occupying about half of the ACS chip. Thus the volume overdensity is a factor of 4. The star formation rate derived from detected sources in this overdense region is sufficient to reionize the local IGM."}],"citation":{"chicago":"Malhotra, S., J. E. Rhoads, N. Pirzkal, Zoltán Haiman, C. Xu, E. Daddi, H. Yan, et al. “An Overdensity of Galaxies at Z= 5.9 ± 0.2 in the Hubble Ultra Deep Field Confirmed Using the ACS Grism.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2005. <a href=\"https://doi.org/10.1086/430047\">https://doi.org/10.1086/430047</a>.","apa":"Malhotra, S., Rhoads, J. E., Pirzkal, N., Haiman, Z., Xu, C., Daddi, E., … di Serego Alighieri, S. (2005). An overdensity of galaxies at z= 5.9 ± 0.2 in the Hubble Ultra Deep Field confirmed using the ACS grism. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1086/430047\">https://doi.org/10.1086/430047</a>","mla":"Malhotra, S., et al. “An Overdensity of Galaxies at Z= 5.9 ± 0.2 in the Hubble Ultra Deep Field Confirmed Using the ACS Grism.” <i>The Astrophysical Journal</i>, vol. 626, no. 2, American Astronomical Society, 2005, pp. 666–79, doi:<a href=\"https://doi.org/10.1086/430047\">10.1086/430047</a>.","ista":"Malhotra S, Rhoads JE, Pirzkal N, Haiman Z, Xu C, Daddi E, Yan H, Bergeron LE, Wang J, Ferguson HC, Gronwall C, Koekemoer A, Kuemmel M, Moustakas LA, Panagia N, Pasquali A, Stiavelli M, Walsh J, Windhorst RA, di Serego Alighieri S. 2005. An overdensity of galaxies at z= 5.9 ± 0.2 in the Hubble Ultra Deep Field confirmed using the ACS grism. The Astrophysical Journal. 626(2), 666–679.","short":"S. Malhotra, J.E. Rhoads, N. Pirzkal, Z. Haiman, C. Xu, E. Daddi, H. Yan, L.E. Bergeron, J. Wang, H.C. Ferguson, C. Gronwall, A. Koekemoer, M. Kuemmel, L.A. Moustakas, N. Panagia, A. Pasquali, M. Stiavelli, J. Walsh, R.A. Windhorst, S. di Serego Alighieri, The Astrophysical Journal 626 (2005) 666–679.","ama":"Malhotra S, Rhoads JE, Pirzkal N, et al. An overdensity of galaxies at z= 5.9 ± 0.2 in the Hubble Ultra Deep Field confirmed using the ACS grism. <i>The Astrophysical Journal</i>. 2005;626(2):666-679. doi:<a href=\"https://doi.org/10.1086/430047\">10.1086/430047</a>","ieee":"S. Malhotra <i>et al.</i>, “An overdensity of galaxies at z= 5.9 ± 0.2 in the Hubble Ultra Deep Field confirmed using the ACS grism,” <i>The Astrophysical Journal</i>, vol. 626, no. 2. American Astronomical Society, pp. 666–679, 2005."},"oa_version":"Published Version","date_updated":"2024-09-30T11:34:11Z","article_type":"original","intvolume":"       626","article_processing_charge":"No","title":"An overdensity of galaxies at z= 5.9 ± 0.2 in the Hubble Ultra Deep Field confirmed using the ACS grism","publisher":"American Astronomical Society","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1086/430047","day":"20","status":"public","publication_status":"published","scopus_import":"1","type":"journal_article","publication":"The Astrophysical Journal","page":"666-679"},{"type":"journal_article","scopus_import":"1","page":"582-586","publication":"The Astrophysical Journal","doi":"10.1086/427622","status":"public","publication_status":"published","day":"10","article_processing_charge":"No","intvolume":"       621","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Astronomical Society","title":"A redshift z≈ 5.4 Lyα emitting galaxy with linear morphology in the GRAPES/Hubble Ultra Deep Field","article_type":"original","date_updated":"2024-09-30T12:17:32Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1086/427622"}],"month":"05","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We have discovered an extended Lyα plume (UDF 5225) associated with a compact source at redshift z ≈ 5.4 in slitless spectroscopic data from the Grism ACS Program for Extragalactic Science (GRAPES) project. The spatial extent of the emission is about 6 × 1.5 kpc (1'' × 0farcs25). Combining our grism data and the broadband images from the Hubble Ultra Deep Field (UDF) images, we find a Lyα line flux of ~2.2 × 10^-17 ergs cm^-2 s^-1 and surface brightness ~7 × 10^-17ergs cm^-2 s-1 arcsec^-2. The UDF images show diffuse continuum emission associated with UDF 5225, including three embedded knots. The morphology of UDF 5225 is highly suggestive of a galaxy in assembly. It is possible that the prominent Lyα emission from this object is due to an active nucleus, and that we are seeing the simultaneous growth through accretion of a galaxy and its central black hole. Follow-up observations at higher spectral resolution could test this hypothesis."}],"citation":{"chicago":"Rhoads, James E., Nino Panagia, Rogier A. Windhorst, Sangeeta Malhotra, Norbert Pirzkal, Chun Xu, Louis Gregory Strolger, et al. “A Redshift Z≈ 5.4 Lyα Emitting Galaxy with Linear Morphology in the GRAPES/Hubble Ultra Deep Field.” <i>The Astrophysical Journal</i>. American Astronomical Society, 2005. <a href=\"https://doi.org/10.1086/427622\">https://doi.org/10.1086/427622</a>.","apa":"Rhoads, J. E., Panagia, N., Windhorst, R. A., Malhotra, S., Pirzkal, N., Xu, C., … Yan, H. (2005). A redshift z≈ 5.4 Lyα emitting galaxy with linear morphology in the GRAPES/Hubble Ultra Deep Field. <i>The Astrophysical Journal</i>. American Astronomical Society. <a href=\"https://doi.org/10.1086/427622\">https://doi.org/10.1086/427622</a>","ista":"Rhoads JE, Panagia N, Windhorst RA, Malhotra S, Pirzkal N, Xu C, Strolger LG, Bergeron LE, Daddi E, Ferguson H, Gardner JP, Gronwall C, Haiman Z, Koekemoer A, Kummel M, Moustakas LA, Pasquali A, Riess A, di Serego Alighieri S, Stiavelli M, Tsvetanov Z, Vernet J, Walsh J, Yan H. 2005. A redshift z≈ 5.4 Lyα emitting galaxy with linear morphology in the GRAPES/Hubble Ultra Deep Field. The Astrophysical Journal. 621(2), 582–586.","mla":"Rhoads, James E., et al. “A Redshift Z≈ 5.4 Lyα Emitting Galaxy with Linear Morphology in the GRAPES/Hubble Ultra Deep Field.” <i>The Astrophysical Journal</i>, vol. 621, no. 2, American Astronomical Society, 2005, pp. 582–86, doi:<a href=\"https://doi.org/10.1086/427622\">10.1086/427622</a>.","short":"J.E. Rhoads, N. Panagia, R.A. Windhorst, S. Malhotra, N. Pirzkal, C. Xu, L.G. Strolger, L.E. Bergeron, E. Daddi, H. Ferguson, J.P. Gardner, C. Gronwall, Z. Haiman, A. Koekemoer, M. Kummel, L.A. Moustakas, A. Pasquali, A. Riess, S. di Serego Alighieri, M. Stiavelli, Z. Tsvetanov, J. Vernet, J. Walsh, H. Yan, The Astrophysical Journal 621 (2005) 582–586.","ama":"Rhoads JE, Panagia N, Windhorst RA, et al. A redshift z≈ 5.4 Lyα emitting galaxy with linear morphology in the GRAPES/Hubble Ultra Deep Field. <i>The Astrophysical Journal</i>. 2005;621(2):582-586. doi:<a href=\"https://doi.org/10.1086/427622\">10.1086/427622</a>","ieee":"J. E. Rhoads <i>et al.</i>, “A redshift z≈ 5.4 Lyα emitting galaxy with linear morphology in the GRAPES/Hubble Ultra Deep Field,” <i>The Astrophysical Journal</i>, vol. 621, no. 2. American Astronomical Society, pp. 582–586, 2005."},"issue":"2","year":"2005","oa":1,"date_created":"2024-09-06T10:15:40Z","language":[{"iso":"eng"}],"extern":"1","quality_controlled":"1","author":[{"last_name":"Rhoads","first_name":"James E.","full_name":"Rhoads, James E."},{"full_name":"Panagia, Nino","first_name":"Nino","last_name":"Panagia"},{"last_name":"Windhorst","first_name":"Rogier A.","full_name":"Windhorst, Rogier A."},{"full_name":"Malhotra, Sangeeta","first_name":"Sangeeta","last_name":"Malhotra"},{"first_name":"Norbert","full_name":"Pirzkal, Norbert","last_name":"Pirzkal"},{"last_name":"Xu","full_name":"Xu, Chun","first_name":"Chun"},{"last_name":"Strolger","first_name":"Louis Gregory","full_name":"Strolger, Louis Gregory"},{"first_name":"Louis E.","full_name":"Bergeron, Louis E.","last_name":"Bergeron"},{"last_name":"Daddi","first_name":"Emanuele","full_name":"Daddi, Emanuele"},{"full_name":"Ferguson, Harry","first_name":"Harry","last_name":"Ferguson"},{"full_name":"Gardner, Jonathan P.","first_name":"Jonathan P.","last_name":"Gardner"},{"last_name":"Gronwall","first_name":"Caryl","full_name":"Gronwall, Caryl"},{"last_name":"Haiman","full_name":"Haiman, Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán"},{"last_name":"Koekemoer","first_name":"Anton","full_name":"Koekemoer, Anton"},{"last_name":"Kummel","full_name":"Kummel, Martin","first_name":"Martin"},{"first_name":"Leonidas A.","full_name":"Moustakas, Leonidas A.","last_name":"Moustakas"},{"last_name":"Pasquali","full_name":"Pasquali, Anna","first_name":"Anna"},{"last_name":"Riess","full_name":"Riess, Adam","first_name":"Adam"},{"last_name":"di Serego Alighieri","first_name":"Sperello","full_name":"di Serego Alighieri, Sperello"},{"last_name":"Stiavelli","first_name":"Massimo","full_name":"Stiavelli, Massimo"},{"full_name":"Tsvetanov, Zlatan","first_name":"Zlatan","last_name":"Tsvetanov"},{"first_name":"Joel","full_name":"Vernet, Joel","last_name":"Vernet"},{"last_name":"Walsh","first_name":"Jeremy","full_name":"Walsh, Jeremy"},{"last_name":"Yan","full_name":"Yan, Haojing","first_name":"Haojing"}],"_id":"17781","publication_identifier":{"issn":["0004-637X","1538-4357"]},"date_published":"2005-05-10T00:00:00Z","volume":621},{"author":[{"last_name":"Haiman","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán","full_name":"Haiman, Zoltán"}],"_id":"17786","date_published":"2005-02-01T00:00:00Z","publication_identifier":{"issn":["0375-9687"]},"volume":158,"month":"02","main_file_link":[{"url":"https://doi.org/10.1143/PTPS.158.86","open_access":"1"}],"abstract":[{"text":"The first stars and black holes that formed in the Universe are likely too faint for a direct detection. However, by ionizing most of the intergalactic medium (IGM), they left an indirect clue that reveals their existence. We discuss currently available observational constraints on the reionization history of IGM, and the extent to which accreting black holes (BHs) and stars can help account for these observations. We argue, based on the combined statistics of Lyman α and β absorption in quasar spectra, that the IGM contains a significant amount of neutral hydrogen with nHI/nH ≳0.1. On the other hand, we argue, based on the lack of a strong evolution in the observed abundance of Lyman α emitting galaxies beyond z ∼5.5, that the mean neutral hydrogen fraction cannot exceed nHI/nH ≈0.3 at the same redshift. We conclude that the IGM is experiencing rapid ionization at redshift z ∼6.\r\nWe find that quasar BHs, including faint ones that are individually below the detection thresholds of existing optical and X-ray surveys, are unlikely to drive the evolution of the neutral fraction around this epoch, because they would over-produce the present-day soft X-ray background. On the other hand, the seeds of the z ∼6 quasar BHs likely appeared at much earlier epochs (z ∼20), and produced hard ionizing radiation by accretion. These early BHs are promising candidates to account for the high redshift (z ∼15) ionization implied by the recent cosmic microwave anisotropy data from WMAP.\r\nUsing a model for the growth of BHs by accretion and mergers in a hierarchical cosmology, we suggest that the early growth of quasars must include a super-Eddington growth phase, and that, although not yet optically identified, the FIRST radio survey may have already detected several thousand > 10^8 M⊙ BHs at z > 6.","lang":"eng"}],"citation":{"chicago":"Haiman, Zoltán. “Finding the First Generation of Stars and Black Holes.” <i>Progress of Theoretical Physics Supplement</i>. Oxford University Press, 2005. <a href=\"https://doi.org/10.1143/ptps.158.86\">https://doi.org/10.1143/ptps.158.86</a>.","mla":"Haiman, Zoltán. “Finding the First Generation of Stars and Black Holes.” <i>Progress of Theoretical Physics Supplement</i>, vol. 158, Oxford University Press, 2005, pp. 86–104, doi:<a href=\"https://doi.org/10.1143/ptps.158.86\">10.1143/ptps.158.86</a>.","apa":"Haiman, Z. (2005). Finding the first generation of stars and black holes. <i>Progress of Theoretical Physics Supplement</i>. Oxford University Press. <a href=\"https://doi.org/10.1143/ptps.158.86\">https://doi.org/10.1143/ptps.158.86</a>","ista":"Haiman Z. 2005. Finding the first generation of stars and black holes. Progress of Theoretical Physics Supplement. 158, 86–104.","short":"Z. Haiman, Progress of Theoretical Physics Supplement 158 (2005) 86–104.","ama":"Haiman Z. Finding the first generation of stars and black holes. <i>Progress of Theoretical Physics Supplement</i>. 2005;158:86-104. doi:<a href=\"https://doi.org/10.1143/ptps.158.86\">10.1143/ptps.158.86</a>","ieee":"Z. Haiman, “Finding the first generation of stars and black holes,” <i>Progress of Theoretical Physics Supplement</i>, vol. 158. Oxford University Press, pp. 86–104, 2005."},"oa_version":"Published Version","year":"2005","oa":1,"quality_controlled":"1","extern":"1","date_created":"2024-09-06T10:19:04Z","language":[{"iso":"eng"}],"intvolume":"       158","article_processing_charge":"No","title":"Finding the first generation of stars and black holes","publisher":"Oxford University Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","date_updated":"2024-09-30T13:00:29Z","scopus_import":"1","type":"journal_article","publication":"Progress of Theoretical Physics Supplement","page":"86-104","doi":"10.1143/ptps.158.86","status":"public","day":"01","publication_status":"published"},{"date_published":"2005-11-16T00:00:00Z","publication_identifier":{"issn":["0270-6474","1529-2401"]},"external_id":{"pmid":["16291952"]},"volume":25,"author":[{"last_name":"Vogels","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","full_name":"Vogels, Tim P"},{"first_name":"L. F.","full_name":"Abbott, L. F.","last_name":"Abbott"}],"_id":"8028","year":"2005","oa":1,"issue":"46","quality_controlled":"1","date_created":"2020-06-25T13:12:33Z","language":[{"iso":"eng"}],"extern":"1","month":"11","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6725859/","open_access":"1"}],"abstract":[{"text":"Transmission of signals within the brain is essential for cognitive function, but it is not clear how neural circuits support reliable and accurate signal propagation over a sufficiently large dynamic range. Two modes of propagation have been studied: synfire chains, in which synchronous activity travels through feedforward layers of a neuronal network, and the propagation of fluctuations in firing rate across these layers. In both cases, a sufficient amount of noise, which was added to previous models from an external source, had to be included to support stable propagation. Sparse, randomly connected networks of spiking model neurons can generate chaotic patterns of activity. We investigate whether this activity, which is a more realistic noise source, is sufficient to allow for signal transmission. We find that, for rate-coded signals but not for synfire chains, such networks support robust and accurate signal reproduction through up to six layers if appropriate adjustments are made in synaptic strengths. We investigate the factors affecting transmission and show that multiple signals can propagate simultaneously along different pathways. Using this feature, we show how different types of logic gates can arise within the architecture of the random network through the strengthening of specific synapses.","lang":"eng"}],"citation":{"short":"T.P. Vogels, L.F. Abbott, Journal of Neuroscience 25 (2005) 10786–10795.","mla":"Vogels, Tim P., and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” <i>Journal of Neuroscience</i>, vol. 25, no. 46, Society for Neuroscience, 2005, pp. 10786–95, doi:<a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">10.1523/jneurosci.3508-05.2005</a>.","ista":"Vogels TP, Abbott LF. 2005. Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. 25(46), 10786–10795.","apa":"Vogels, T. P., &#38; Abbott, L. F. (2005). Signal propagation and logic gating in networks of integrate-and-fire neurons. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">https://doi.org/10.1523/jneurosci.3508-05.2005</a>","chicago":"Vogels, Tim P, and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2005. <a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">https://doi.org/10.1523/jneurosci.3508-05.2005</a>.","ieee":"T. P. Vogels and L. F. Abbott, “Signal propagation and logic gating in networks of integrate-and-fire neurons,” <i>Journal of Neuroscience</i>, vol. 25, no. 46. Society for Neuroscience, pp. 10786–10795, 2005.","ama":"Vogels TP, Abbott LF. Signal propagation and logic gating in networks of integrate-and-fire neurons. <i>Journal of Neuroscience</i>. 2005;25(46):10786-10795. doi:<a href=\"https://doi.org/10.1523/jneurosci.3508-05.2005\">10.1523/jneurosci.3508-05.2005</a>"},"oa_version":"Published Version","article_type":"original","date_updated":"2021-01-12T08:16:37Z","pmid":1,"intvolume":"        25","article_processing_charge":"No","publisher":"Society for Neuroscience","title":"Signal propagation and logic gating in networks of integrate-and-fire neurons","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","doi":"10.1523/jneurosci.3508-05.2005","status":"public","day":"16","publication_status":"published","type":"journal_article","publication":"Journal of Neuroscience","page":"10786-10795"},{"year":"2005","issue":"1","quality_controlled":"1","extern":"1","date_created":"2020-06-25T13:13:11Z","language":[{"iso":"eng"}],"month":"07","citation":{"short":"T.P. Vogels, K. Rajan, L.F. Abbott, Annual Review of Neuroscience 28 (2005) 357–376.","ista":"Vogels TP, Rajan K, Abbott LF. 2005. Neural network dynamics. Annual Review of Neuroscience. 28(1), 357–376.","mla":"Vogels, Tim P., et al. “Neural Network Dynamics.” <i>Annual Review of Neuroscience</i>, vol. 28, no. 1, Annual Reviews, 2005, pp. 357–76, doi:<a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">10.1146/annurev.neuro.28.061604.135637</a>.","apa":"Vogels, T. P., Rajan, K., &#38; Abbott, L. F. (2005). Neural network dynamics. <i>Annual Review of Neuroscience</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">https://doi.org/10.1146/annurev.neuro.28.061604.135637</a>","chicago":"Vogels, Tim P, Kanaka Rajan, and L.F. Abbott. “Neural Network Dynamics.” <i>Annual Review of Neuroscience</i>. Annual Reviews, 2005. <a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">https://doi.org/10.1146/annurev.neuro.28.061604.135637</a>.","ieee":"T. P. Vogels, K. Rajan, and L. F. Abbott, “Neural network dynamics,” <i>Annual Review of Neuroscience</i>, vol. 28, no. 1. Annual Reviews, pp. 357–376, 2005.","ama":"Vogels TP, Rajan K, Abbott LF. Neural network dynamics. <i>Annual Review of Neuroscience</i>. 2005;28(1):357-376. doi:<a href=\"https://doi.org/10.1146/annurev.neuro.28.061604.135637\">10.1146/annurev.neuro.28.061604.135637</a>"},"abstract":[{"lang":"eng","text":"Neural network modeling is often concerned with stimulus-driven responses, but most of the activity in the brain is internally generated. Here, we review network models of internally generated activity, focusing on three types of network dynamics: (a) sustained responses to transient stimuli, which provide a model of working memory; (b) oscillatory network activity; and (c) chaotic activity, which models complex patterns of background spiking in cortical and other circuits. We also review propagation of stimulus-driven activity through spontaneously active networks. Exploring these aspects of neural network dynamics is critical for understanding how neural circuits produce cognitive function."}],"oa_version":"None","date_published":"2005-07-21T00:00:00Z","publication_identifier":{"issn":["0147-006X","1545-4126"]},"external_id":{"pmid":["16022600"]},"volume":28,"author":[{"last_name":"Vogels","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","full_name":"Vogels, Tim P"},{"last_name":"Rajan","full_name":"Rajan, Kanaka","first_name":"Kanaka"},{"first_name":"L.F.","full_name":"Abbott, L.F.","last_name":"Abbott"}],"_id":"8029","doi":"10.1146/annurev.neuro.28.061604.135637","publication_status":"published","status":"public","day":"21","type":"journal_article","publication":"Annual Review of Neuroscience","page":"357-376","article_type":"review","date_updated":"2021-01-12T08:16:37Z","pmid":1,"intvolume":"        28","article_processing_charge":"No","title":"Neural network dynamics","publisher":"Annual Reviews","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425"},{"volume":14,"date_published":"2005-11-01T00:00:00Z","date_updated":"2021-01-12T08:19:13Z","title":"Distribution of the strength of selection against amino acid replacements in human proteins","publisher":"Oxford University Press","publist_id":"6807","intvolume":"        14","_id":"843","author":[{"last_name":"Yampolsky","full_name":"Yampolsky, Lev Y","first_name":"Lev"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"}],"quality_controlled":0,"extern":1,"date_created":"2018-12-11T11:48:48Z","publication_status":"published","day":"01","status":"public","year":"2005","doi":"10.1093/hmg/ddi350","issue":"21","publication":"Human Molecular Genetics","citation":{"chicago":"Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” <i>Human Molecular Genetics</i>. Oxford University Press, 2005. <a href=\"https://doi.org/10.1093/hmg/ddi350\">https://doi.org/10.1093/hmg/ddi350</a>.","mla":"Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” <i>Human Molecular Genetics</i>, vol. 14, no. 21, Oxford University Press, 2005, pp. 3191–201, doi:<a href=\"https://doi.org/10.1093/hmg/ddi350\">10.1093/hmg/ddi350</a>.","apa":"Yampolsky, L., Kondrashov, F., &#38; Kondrashov, A. (2005). Distribution of the strength of selection against amino acid replacements in human proteins. <i>Human Molecular Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/hmg/ddi350\">https://doi.org/10.1093/hmg/ddi350</a>","ista":"Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 14(21), 3191–3201.","short":"L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005) 3191–3201.","ama":"Yampolsky L, Kondrashov F, Kondrashov A. Distribution of the strength of selection against amino acid replacements in human proteins. <i>Human Molecular Genetics</i>. 2005;14(21):3191-3201. doi:<a href=\"https://doi.org/10.1093/hmg/ddi350\">10.1093/hmg/ddi350</a>","ieee":"L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength of selection against amino acid replacements in human proteins,” <i>Human Molecular Genetics</i>, vol. 14, no. 21. Oxford University Press, pp. 3191–3201, 2005."},"abstract":[{"lang":"eng","text":"The impact of an amino acid replacement on the organism's fitness can vary from lethal to selectively neutral and even, in rare cases, beneficial. Substantial data are available on either pathogenic or acceptable replacements. However, the whole distribution of coefficients of selection against individual replacements is not known for any organism. To ascertain this distribution for human proteins, we combined data on pathogenic missense mutations, on human non-synonymous SNPs and on human-chimpanzee divergence of orthologous proteins. Fractions of amino acid replacements which reduce fitness by &gt;10-2, 10-2-10-4, 10-4-10-5 and &lt;10-5 are 25, 49, 14 and 12%, respectively. On average, the strength of selection against a replacement is substantially higher when chemically dissimilar amino acids are involved, and the Grantham's index of a replacement explains 35% of variance in the average logarithm of selection coefficients associated with different replacements. Still, the impact of a replacement depends on its context within the protein more than on its own nature. Reciprocal replacements are often associated with rather different selection coefficients, in particular, replacements of non-polar amino acids with polar ones are typically much more deleterious than replacements in the opposite direction. However, differences between evolutionary fluxes of reciprocal replacements are only weakly correlated with the differences between the corresponding selection coefficients."}],"page":"3191 - 3201","month":"11","type":"journal_article"},{"publication_identifier":{"issn":["0925-2738","1573-5001"]},"date_updated":"2021-01-12T08:19:38Z","article_type":"original","date_published":"2005-12-01T00:00:00Z","volume":33,"keyword":["Spectroscopy","Biochemistry"],"article_processing_charge":"No","_id":"8491","author":[{"orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Ēriks","full_name":"Kupče, Ēriks","last_name":"Kupče"},{"first_name":"Bernhard","full_name":"Brutscher, Bernhard","last_name":"Brutscher"}],"intvolume":"        33","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","title":"SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds","issue":"4","doi":"10.1007/s10858-005-4425-x","year":"2005","day":"01","publication_status":"published","date_created":"2020-09-18T10:13:59Z","language":[{"iso":"eng"}],"status":"public","extern":"1","quality_controlled":"1","type":"journal_article","month":"12","oa_version":"None","page":"199-211","citation":{"ieee":"P. Schanda, Ē. Kupče, and B. Brutscher, “SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds,” <i>Journal of Biomolecular NMR</i>, vol. 33, no. 4. Springer Nature, pp. 199–211, 2005.","ama":"Schanda P, Kupče Ē, Brutscher B. SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. <i>Journal of Biomolecular NMR</i>. 2005;33(4):199-211. doi:<a href=\"https://doi.org/10.1007/s10858-005-4425-x\">10.1007/s10858-005-4425-x</a>","short":"P. Schanda, Ē. Kupče, B. Brutscher, Journal of Biomolecular NMR 33 (2005) 199–211.","apa":"Schanda, P., Kupče, Ē., &#38; Brutscher, B. (2005). SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-005-4425-x\">https://doi.org/10.1007/s10858-005-4425-x</a>","mla":"Schanda, Paul, et al. “SOFAST-HMQC Experiments for Recording Two-Dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds.” <i>Journal of Biomolecular NMR</i>, vol. 33, no. 4, Springer Nature, 2005, pp. 199–211, doi:<a href=\"https://doi.org/10.1007/s10858-005-4425-x\">10.1007/s10858-005-4425-x</a>.","ista":"Schanda P, Kupče Ē, Brutscher B. 2005. SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. Journal of Biomolecular NMR. 33(4), 199–211.","chicago":"Schanda, Paul, Ēriks Kupče, and Bernhard Brutscher. “SOFAST-HMQC Experiments for Recording Two-Dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2005. <a href=\"https://doi.org/10.1007/s10858-005-4425-x\">https://doi.org/10.1007/s10858-005-4425-x</a>."},"abstract":[{"text":"Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H–15N correlation spectra in a few seconds of acquisition time using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005) J. Am. Chem. Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC to record 1H–15N and 1H−13C correlation spectra of proteins of different size and at different magnetic field strengths. Compared to standard 1H–15N correlation experiments SOFAST-HMQC provides a significant gain in sensitivity, especially for fast repetition rates. Guidelines are provided on how to set up SOFAST-HMQC experiments for a given protein sample. In addition, an alternative pulse scheme, IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped with cryogenic probes, and fast measurement of one-bond 1H–13C and 1H–15N scalar and residual dipolar coupling constants.","lang":"eng"}],"publication":"Journal of Biomolecular NMR"},{"article_processing_charge":"No","_id":"8492","author":[{"full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"}],"intvolume":"       127","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Chemical Society","title":"Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds","date_updated":"2021-01-12T08:19:39Z","publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_type":"original","date_published":"2005-05-14T00:00:00Z","volume":127,"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"type":"journal_article","month":"05","oa_version":"None","page":"8014-8015","abstract":[{"lang":"eng","text":"We demonstrate for different protein samples that 2D 1H−15N correlation NMR spectra can be recorded in a few seconds of acquisition time using a new band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence experiment. This has enabled us to measure fast hydrogen−deuterium exchange rate constants along the backbone of a small globular protein fragment by real-time 2D NMR."}],"citation":{"chicago":"Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of Seconds.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2005. <a href=\"https://doi.org/10.1021/ja051306e\">https://doi.org/10.1021/ja051306e</a>.","mla":"Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of Seconds.” <i>Journal of the American Chemical Society</i>, vol. 127, no. 22, American Chemical Society, 2005, pp. 8014–15, doi:<a href=\"https://doi.org/10.1021/ja051306e\">10.1021/ja051306e</a>.","ista":"Schanda P, Brutscher B. 2005. Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. Journal of the American Chemical Society. 127(22), 8014–8015.","apa":"Schanda, P., &#38; Brutscher, B. (2005). Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja051306e\">https://doi.org/10.1021/ja051306e</a>","short":"P. Schanda, B. Brutscher, Journal of the American Chemical Society 127 (2005) 8014–8015.","ama":"Schanda P, Brutscher B. Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. <i>Journal of the American Chemical Society</i>. 2005;127(22):8014-8015. doi:<a href=\"https://doi.org/10.1021/ja051306e\">10.1021/ja051306e</a>","ieee":"P. Schanda and B. Brutscher, “Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds,” <i>Journal of the American Chemical Society</i>, vol. 127, no. 22. American Chemical Society, pp. 8014–8015, 2005."},"publication":"Journal of the American Chemical Society","issue":"22","doi":"10.1021/ja051306e","year":"2005","publication_status":"published","day":"14","date_created":"2020-09-18T10:14:05Z","language":[{"iso":"eng"}],"status":"public","extern":"1","quality_controlled":"1"},{"year":"2005","issue":"1","doi":"10.1016/j.jfa.2004.09.006","quality_controlled":"1","day":"01","publication_status":"published","language":[{"iso":"eng"}],"date_created":"2020-09-18T10:49:06Z","status":"public","extern":"1","month":"12","type":"journal_article","citation":{"ieee":"J. Bourgain and V. Kaloshin, “On diffusion in high-dimensional Hamiltonian systems,” <i>Journal of Functional Analysis</i>, vol. 229, no. 1. Elsevier, pp. 1–61, 2005.","ama":"Bourgain J, Kaloshin V. On diffusion in high-dimensional Hamiltonian systems. <i>Journal of Functional Analysis</i>. 2005;229(1):1-61. doi:<a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">10.1016/j.jfa.2004.09.006</a>","short":"J. Bourgain, V. Kaloshin, Journal of Functional Analysis 229 (2005) 1–61.","chicago":"Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” <i>Journal of Functional Analysis</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">https://doi.org/10.1016/j.jfa.2004.09.006</a>.","mla":"Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” <i>Journal of Functional Analysis</i>, vol. 229, no. 1, Elsevier, 2005, pp. 1–61, doi:<a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">10.1016/j.jfa.2004.09.006</a>.","apa":"Bourgain, J., &#38; Kaloshin, V. (2005). On diffusion in high-dimensional Hamiltonian systems. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">https://doi.org/10.1016/j.jfa.2004.09.006</a>","ista":"Bourgain J, Kaloshin V. 2005. On diffusion in high-dimensional Hamiltonian systems. Journal of Functional Analysis. 229(1), 1–61."},"abstract":[{"lang":"eng","text":"The purpose of this paper is to construct examples of diffusion for E-Hamiltonian perturbations\r\nof completely integrable Hamiltonian systems in 2d-dimensional phase space, with d large.\r\nIn the first part of the paper, simple and explicit examples are constructed illustrating absence\r\nof ‘long-time’ stability for size E Hamiltonian perturbations of quasi-convex integrable systems\r\nalready when the dimension 2d of phase space becomes as large as log 1/E . We first produce\r\nthe example in Gevrey class and then a real analytic one, with some additional work.\r\nIn the second part, we consider again E-Hamiltonian perturbations of completely integrable\r\nHamiltonian system in 2d-dimensional space with E-small but not too small, |E| > exp(−d), with\r\nd the number of degrees of freedom assumed large. It is shown that for a class of analytic\r\ntime-periodic perturbations, there exist linearly diffusing trajectories. The underlying idea for\r\nboth examples is similar and consists in coupling a fixed degree of freedom with a large\r\nnumber of them. The procedure and analytical details are however significantly different. As\r\nmentioned, the construction in Part I is totally elementary while Part II is more involved, relying\r\nin particular on the theory of normally hyperbolic invariant manifolds, methods of generating\r\nfunctions, Aubry–Mather theory, and Mather’s variational methods."}],"publication":"Journal of Functional Analysis","oa_version":"None","page":"1-61","date_published":"2005-12-01T00:00:00Z","date_updated":"2021-01-12T08:19:49Z","publication_identifier":{"issn":["0022-1236"]},"article_type":"original","volume":229,"keyword":["Analysis"],"_id":"8516","author":[{"full_name":"Bourgain, Jean","first_name":"Jean","last_name":"Bourgain"},{"orcid":"0000-0002-6051-2628","last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim"}],"intvolume":"       229","article_processing_charge":"No","publisher":"Elsevier","title":"On diffusion in high-dimensional Hamiltonian systems","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"pmid":1,"intvolume":"        50","article_processing_charge":"No","publisher":"Pleiades Publishing","title":"The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6769","article_type":"original","date_updated":"2021-01-12T08:21:01Z","type":"journal_article","publication":"Biofizika","page":"389 - 395","day":"01","publication_status":"published","status":"public","author":[{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"}],"_id":"877","date_published":"2005-05-01T00:00:00Z","external_id":{"pmid":["15977826"]},"volume":50,"month":"05","main_file_link":[{"url":"http://pleiades.online/abstract/biophys/5/biophys0349_abstract.pdf"}],"abstract":[{"text":"Sequence analysis of protein and mitochondrially encoded tRNA genes shows that substitutions\r\nproducing pathogenic effects in humans are often found in normal, healthy individuals from other species.\r\nAnalysis of stability of protein and tRNA structures shows that the disease-causing effects of pathogenic\r\nmutations can be neutralized by other, compensatory substitutions that restore the structural stability of the\r\nmolecule. Further study of such substitutions will, hopefully, lead to new methods for curing genetic dis-\r\neases that may be based on the correction of molecule stability as a whole instead of reversing an individual\r\npathogenic mutation.","lang":"eng"}],"citation":{"chicago":"Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” <i>Biofizika</i>. Pleiades Publishing, 2005.","mla":"Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” <i>Biofizika</i>, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 389–95.","ista":"Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 50(3), 389–395.","apa":"Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. <i>Biofizika</i>. Pleiades Publishing.","short":"F. Kondrashov, Biofizika 50 (2005) 389–395.","ama":"Kondrashov F. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. <i>Biofizika</i>. 2005;50(3):389-395.","ieee":"F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” <i>Biofizika</i>, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005."},"oa_version":"None","year":"2005","issue":"3","quality_controlled":"1","date_created":"2018-12-11T11:48:58Z","language":[{"iso":"eng"}],"extern":"1"},{"publist_id":"6770","title":"In search of the limits of evolution","publisher":"Nature Publishing Group","intvolume":"        37","_id":"878","author":[{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Fyodor Kondrashov"}],"volume":37,"date_updated":"2021-01-12T08:21:02Z","date_published":"2005-01-01T00:00:00Z","page":"9 - 10","publication":"Nature Genetics","abstract":[{"text":"Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions.\n","lang":"eng"}],"citation":{"ieee":"F. Kondrashov, “In search of the limits of evolution,” <i>Nature Genetics</i>, vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005.","ama":"Kondrashov F. In search of the limits of evolution. <i>Nature Genetics</i>. 2005;37(1):9-10. doi:<a href=\"https://doi.org/10.1038/ng0105-9\">10.1038/ng0105-9</a>","short":"F. Kondrashov, Nature Genetics 37 (2005) 9–10.","chicago":"Kondrashov, Fyodor. “In Search of the Limits of Evolution.” <i>Nature Genetics</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/ng0105-9\">https://doi.org/10.1038/ng0105-9</a>.","ista":"Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics. 37(1), 9–10.","mla":"Kondrashov, Fyodor. “In Search of the Limits of Evolution.” <i>Nature Genetics</i>, vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:<a href=\"https://doi.org/10.1038/ng0105-9\">10.1038/ng0105-9</a>.","apa":"Kondrashov, F. (2005). In search of the limits of evolution. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng0105-9\">https://doi.org/10.1038/ng0105-9</a>"},"type":"journal_article","month":"01","extern":1,"status":"public","date_created":"2018-12-11T11:48:59Z","day":"01","publication_status":"published","quality_controlled":0,"doi":"10.1038/ng0105-9","issue":"1","year":"2005"},{"citation":{"ieee":"F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” <i>Biofizika</i>, vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005.","ama":"Kondrashov F. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. <i>Biofizika</i>. 2005;50(3):396-403.","short":"F. Kondrashov, Biofizika 50 (2005) 396–403.","chicago":"Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” <i>Biofizika</i>. Pleiades Publishing, 2005.","ista":"Kondrashov F. 2005. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 50(3), 396–403.","mla":"Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” <i>Biofizika</i>, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 396–403.","apa":"Kondrashov, F. (2005). The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. <i>Biofizika</i>. Pleiades Publishing."},"abstract":[{"lang":"eng","text":"Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY). Such evolution sheds light on the relationship between structure and function of tRNA molecules and its impact on the patterns of molecular evolution."}],"publication":"Biofizika","page":"396 - 403","oa_version":"None","month":"05","type":"journal_article","main_file_link":[{"url":"http://pleiades.online/abstract/biophys/5/biophys0356_abstract.pdf"}],"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:48:59Z","status":"public","day":"01","publication_status":"published","extern":"1","year":"2005","issue":"3","publisher":"Pleiades Publishing","title":"The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6768","_id":"880","author":[{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"intvolume":"        50","pmid":1,"article_processing_charge":"No","volume":50,"external_id":{"pmid":["15977827"]},"date_published":"2005-05-01T00:00:00Z","date_updated":"2021-01-12T08:21:07Z"},{"volume":14,"date_published":"2005-08-15T00:00:00Z","date_updated":"2021-01-12T08:21:10Z","publisher":"Oxford University Press","title":"Prediction of pathogenic mutations in mitochondrially encoded human tRNAs","publist_id":"6767","author":[{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"_id":"882","intvolume":"        14","quality_controlled":0,"date_created":"2018-12-11T11:49:00Z","day":"15","status":"public","publication_status":"published","extern":1,"year":"2005","issue":"16","doi":"10.1093/hmg/ddi243","abstract":[{"lang":"eng","text":"Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify ∼90% of all known pathogenic mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively."}],"citation":{"ieee":"F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded human tRNAs,” <i>Human Molecular Genetics</i>, vol. 14, no. 16. Oxford University Press, pp. 2415–2419, 2005.","ama":"Kondrashov F. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. <i>Human Molecular Genetics</i>. 2005;14(16):2415-2419. doi:<a href=\"https://doi.org/10.1093/hmg/ddi243\">10.1093/hmg/ddi243</a>","short":"F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.","apa":"Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. <i>Human Molecular Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/hmg/ddi243\">https://doi.org/10.1093/hmg/ddi243</a>","mla":"Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” <i>Human Molecular Genetics</i>, vol. 14, no. 16, Oxford University Press, 2005, pp. 2415–19, doi:<a href=\"https://doi.org/10.1093/hmg/ddi243\">10.1093/hmg/ddi243</a>.","ista":"Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419.","chicago":"Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” <i>Human Molecular Genetics</i>. Oxford University Press, 2005. <a href=\"https://doi.org/10.1093/hmg/ddi243\">https://doi.org/10.1093/hmg/ddi243</a>."},"publication":"Human Molecular Genetics","page":"2415 - 2419","acknowledgement":"The author thanks P. Andolfatto, D. Bachtrog, N. Esipova, S. Makeev, A. Kondrashov, V. Ramensky, V. Tumanyan and P. Vlasov for a critical reading of the manuscript. The author is an NSF Graduate Research Fellow. This work was supported by a Contract of the Russian Ministry of Science and Education (02.434.11.1008) and a grant on Molecular and Cellular Biology from RAS.\n","month":"08","type":"journal_article"},{"author":[{"first_name":"Ingo","full_name":"Jordan, Ingo K","last_name":"Jordan"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"},{"full_name":"Adzhubeǐ, Ivan A","first_name":"Ivan","last_name":"Adzhubeǐ"},{"first_name":"Yuri","full_name":"Wolf, Yuri I","last_name":"Wolf"},{"last_name":"Koonin","full_name":"Koonin, Eugene V","first_name":"Eugene"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey S"},{"full_name":"Sunyaev, Shamil R","first_name":"Shamil","last_name":"Sunyaev"}],"_id":"893","intvolume":"       433","publisher":"Nature Publishing Group","title":"A universal trend of amino acid gain and loss in protein evolution","publist_id":"6757","date_published":"2005-02-10T00:00:00Z","date_updated":"2021-01-12T08:21:23Z","volume":433,"acknowledgement":"S.S. and I.A.A. were supported by the Genome Canada Foundation.","month":"02","type":"journal_article","citation":{"chicago":"Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin, Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” <i>Nature</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/nature03306\">https://doi.org/10.1038/nature03306</a>.","mla":"Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” <i>Nature</i>, vol. 433, no. 7026, Nature Publishing Group, 2005, pp. 633–38, doi:<a href=\"https://doi.org/10.1038/nature03306\">10.1038/nature03306</a>.","apa":"Jordan, I., Kondrashov, F., Adzhubeǐ, I., Wolf, Y., Koonin, E., Kondrashov, A., &#38; Sunyaev, S. (2005). A universal trend of amino acid gain and loss in protein evolution. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature03306\">https://doi.org/10.1038/nature03306</a>","ista":"Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature. 433(7026), 633–638.","short":"I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov, S. Sunyaev, Nature 433 (2005) 633–638.","ama":"Jordan I, Kondrashov F, Adzhubeǐ I, et al. A universal trend of amino acid gain and loss in protein evolution. <i>Nature</i>. 2005;433(7026):633-638. doi:<a href=\"https://doi.org/10.1038/nature03306\">10.1038/nature03306</a>","ieee":"I. Jordan <i>et al.</i>, “A universal trend of amino acid gain and loss in protein evolution,” <i>Nature</i>, vol. 433, no. 7026. Nature Publishing Group, pp. 633–638, 2005."},"abstract":[{"text":"Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich) genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.","lang":"eng"}],"publication":"Nature","page":"633 - 638","year":"2005","issue":"7026","doi":"10.1038/nature03306","quality_controlled":0,"status":"public","date_created":"2018-12-11T11:49:03Z","day":"10","publication_status":"published","extern":1},{"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"date_published":"2005-01-26T00:00:00Z","department":[{"_id":"DaZi"}],"external_id":{"pmid":["15668172 "]},"volume":15,"_id":"9491","author":[{"full_name":"Tran, Robert K.","first_name":"Robert K.","last_name":"Tran"},{"last_name":"Henikoff","first_name":"Jorja G.","full_name":"Henikoff, Jorja G."},{"full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649"},{"last_name":"Ditt","first_name":"Renata F.","full_name":"Ditt, Renata F."},{"full_name":"Jacobsen, Steven E.","first_name":"Steven E.","last_name":"Jacobsen"},{"first_name":"Steven","full_name":"Henikoff, Steven","last_name":"Henikoff"}],"issue":"2","oa":1,"year":"2005","language":[{"iso":"eng"}],"date_created":"2021-06-07T10:24:30Z","extern":"1","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2005.01.008"}],"month":"01","oa_version":"Published Version","citation":{"short":"R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff, Current Biology 15 (2005) 154–159.","ista":"Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 15(2), 154–159.","mla":"Tran, Robert K., et al. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” <i>Current Biology</i>, vol. 15, no. 2, Elsevier, 2005, pp. 154–59, doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">10.1016/j.cub.2005.01.008</a>.","apa":"Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E., &#38; Henikoff, S. (2005). DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">https://doi.org/10.1016/j.cub.2005.01.008</a>","chicago":"Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” <i>Current Biology</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">https://doi.org/10.1016/j.cub.2005.01.008</a>.","ieee":"R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes,” <i>Current Biology</i>, vol. 15, no. 2. Elsevier, pp. 154–159, 2005.","ama":"Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. <i>Current Biology</i>. 2005;15(2):154-159. doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">10.1016/j.cub.2005.01.008</a>"},"abstract":[{"text":"Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA [1]. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5′ end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic, the appearance of CG methylation clusters over evolutionary time predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G trinucleotides within transcribed regions. This is exactly what we find, implying that CG methylation clusters have contributed profoundly to plant gene evolution. We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units.","lang":"eng"}],"article_type":"original","date_updated":"2021-12-14T09:12:26Z","article_processing_charge":"No","intvolume":"        15","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Elsevier","title":"DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes","doi":"10.1016/j.cub.2005.01.008","status":"public","day":"26","publication_status":"published","type":"journal_article","scopus_import":"1","page":"154-159","publication":"Current Biology"}]