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CLAMATO2017: IGM Lyman-alpha Forest Tomography Survey Public Data Release of Spectra and Maps
<p><strong>CLAMATO 2017 Data Release 1 </strong></p> <p>Public release: 2017 October 9</p> <p>Uploaded to Zenodo on 2018 June 19th after acceptance for publication in ApJS</p> <p>By Khee-Gan Lee (kglee@lbl.gov) and collaborators</p> <p>Supporting paper: https://arxiv.org/abs/1710.02894</p> <p>These are data products associated with the first data release of the COSMOS Lyman-Alpha Mapping And Tomography Observations (CLAMATO) survey with the Keck-I telescope, which mapped 3D Lyman-alpha forest absorption at 2.05<z<2.55 within the COSMOS field.</p> <p>The following is the summary of the main products:<br> - Source catalog (CL2017_VALUEADDED_RELEASE_20171009.TXT)<br> - Reduced spectra, in /spec_v0/ (blue) and /spec_v0_red (red) sub-directories<br> - Continuum-fitted 2.05<z<2.55 Lyman-alpha forest pixel data (pixel_data.bin)<br> - Wiener-reconstructed 3D absorption map (map_2017_v3.bin)</p> <p>Versions:<br> v0 (not public): Initial rough extraction for 2.15<z<2.55 <br> v1 (not public): Extended redshift range to 2.05<z<2.55 <br> v2 (not public): Caught bug that caused wrong [RA,Dec] for ~4-5 objects<br> v3 (released 2017 Oct 9): Fixed bug that caused wrong aspect ratio in output map<br> v4 (released 2018 Mar 29): Fixed bug that caused negative continua in some spectra</p> <p><br> <strong>Redshift Catalog and Spectra</strong> </p> <p>We provide our redshift catalog and reduced spectra obtained with Keck-I/LRIS</p> <p>The source catalog is provided in the ASCII file CL2017_VALUEADDED_RELEASE_20171009.TXT, with the following columns:</p> <p>- BLUE_SPEC: Blue spectrum filename (in /spec_v0/ sub-directory)<br> - TOMO_ID: CLAMATO ID number<br> - GMAG: g-magnitude (AB) per Capak et al 2007 photometric catalog<br> - CONF: Redshift confidence grade: see https://arxiv.org/abs/1710.02894<br> - ZSPEC: Spectroscopic redshift as determined from CLAMATO spectrum<br> - QSO: QSO flag (1 if QSO, 0 if non-QSO)<br> - RA: R.A. in degrees (J2000)<br> - DEC: Dec in degrees (J2000)<br> - S/N_1: Estimated Lya-forest S/N at 2.05<z<2.15, -9.0 denotes no estimate<br> - S/N_2: Estimated Lya-forest S/N at 2.15<z<2.35, -9.0 denotes no estimate<br> - S/N_2: Estimated Lya-forest S/N at 2.35<z<2.55, -9.0 denotes no estimate<br> - S/N_RED: Estimated S/N over restframe 1250 ang < lambda < 1350 ang, -9.0 denotes no estimate<br> - TOMOFLAG: Flag on whether sightline was used in tomographic map (0 for no, 1 for yes)<br> - EXPTIME: Exposure time on the spectrum, in seconds (aggregate)<br> - RED_SPEC: Red spectrum filename (in /spec_v0_red/ sub-directory), 'NA' if doesn't exist</p> <p>The tarballs spec_v0.tar.gz and spec_v0_red.tar.gz include all the reduced spectra from LRIS-Blue and LRIS-Red, respectively.</p> <p>The individual LRIS spectra are provided in FITS format, with the following HDU Extensions:<br> - HDU0: Object spectral flux density, in units of 10^{-17} ergs/s/cm^2/angstrom<br> - HDU1: Noise standard deviation<br> - HDU2: Pixel Wavelengths in angstroms</p> <p><strong>Pixel Data </strong></p> <p>The binary file PIXEL_DATA_v4.BIN stores the concatenated Lyman-alpha forest pixels at 2.05<z<2.55 that have been extracted from the 1D spectra and continuum-fitted. </p> <p>The first value in the binary is a 32-bit integer specifying the number of pixels (64332), followed by 5 double-precision floating point (64-bit) vectors storing the x, y, z, sigma_f, and delta_f of the pixels.</p> <p>An example python script to read pixel_data is as follows:<br> import numpy as np<br> with open('CLAMATO2017_public/pixel_data_v4.bin','r') as f:<br> npix = np.fromfile(f, dtype=np.int32, count=1)<br> f.seek(4)<br> pixel_data = np.fromfile(f,dtype=np.float64).reshape((npix,5))</p> <p>LIST_TOMO_INPUT_2017.TXT is a summary file of corresponding to PIXEL_DATA.BIN, listing the [x,y,z] position of the sightlines that contributed to the file as well as, in the final two columns, the index range that can be used to grab the relevant pixels from the concatenated pixel list.</p> <p><strong>Tomographic Map</strong></p> <p>The Wiener-reconstructed map of the 2.05<z<2.55 IGM within the CLAMATO field is the result of applying the dachshund algorithm (http://github.com/caseywstark/dachshund) to PIXEL_DATA.BIN, with the configuration file INPUT.CFG . (Caveat: the version of PIXEL_DATA.BIN here is not actually the right version to directly input into the dachshund code: the first integer in this file should not be present for input to dachshund). </p> <p>The reconstructed map is MAP_2017_V4.BIN, which is a 60x48x876 = 2552880 pixel double-precision binary with. The dimension that changes fastest is the z-dimension (876 pixels per dimension), followed by the y-dimension (48 pixels per dimension) and x-dimension (60 per dimension).</p> <p>Each map pixel represents a 0.5Mpc/h comoving voxel of the Ly-alpha forest absorption. See the Appendix of https://arxiv.org/abs/1710.02894 for the conversion factors to assume to switch between pixel/voxel and [RA, Dec, redshift].</p> <p>The file MAP_2017_V4_SM2.0.BIN is the same map, but smoothed with a R=2Mpc/h Gaussian kernel.</p>
FIGURE 4. IGM 100 in A Second Specimen of Citipati osmolskae Associated with a Nest of Eggs from Ukhaa Tolgod, Omnogov Aimag, Mongolia
FIGURE 4. IGM 100/1004. An adult Citipati osmolskae collected in 1995 from the Death Row sublocality at Ukhaa Tolgod, Omnogov Aimag, Mongolia, in dorsal view (opposite page and above).
FIGURE 2. IGM 100 in A Second Specimen of Citipati osmolskae Associated with a Nest of Eggs from Ukhaa Tolgod, Omnogov Aimag, Mongolia
FIGURE 2. IGM 100/979. The nesting Citipati osmolskae as it was first found at Ukhaa Tolgod in 1993. Left Amy Davidson, right Louis Chiappe.
IGM Population of HFF structures using Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE data
<p>This repository accompanies the manuscript "<strong>Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations</strong>", to appear in Nat. Methods (2022), see also https://www.biorxiv.org/content/10.1101/2021.08.22.457288v1.</p> <p>It contains the preprocessed input data files (Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE) for the HFF fibroblast cell line to be used in the Integrative Genome Modeling platform (IGM) developed in the Alber lab at UCLA (https://github.com/alberlab/igm).</p> <p>Also, we provide the configuration file to run IGM with those datasets, as we did in generating the HDSF population discussed in the accompanying manuscript. Such population is also provided as an "hss" file. Documentation and a simple demo/tutorial on how IGM can be run is given on the Alber lab Github @ https://github.com/alberlab/igm.</p> <p>All files can be read in using the <em>h5py</em> and <em>alabtools</em> (available @https://github.com/alberlab/alabtools) Python packages. More detailed information is provided in the manuscript and associated Supplementary Information file. </p> <p>For any inquiry/suggestions/doubts please reach out to Lorenzo Boninsegna (bonimba@g.ucla.edu) or Dr. Frank Alber (falber@g.ucla.edu).</p> <p> </p>
Dataset: IGM Biosciences, Inc. (IGMS) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
FIGURE 3. IGM 13117 in A Pliocene goodeid fish of the Paleolake Amajac, Sanctórum, Hidalgo, Mexico
FIGURE 3. IGM 13117, holotype of Paleocharacodon guzmanae gen. and sp. nov., a pregnant female specimen from the Pliocene lacustrine sediments of the Paleolake Amajac, Sanctórum, Atotonilco El Grande Municipality, Hidalgo, central Mexico. A) Part of the specimen observed in white light. B) Part of the specimen observed under UV light. C) Counterpart of the specimen observed under UV light.
FIGURE 4. IGM 11463 in Vaquerosella perrillatae sp. nov.: A Miocene species of Echinarachniidae (Echinodermata: Clypeasteroida) from Baja California Sur, Mexico
FIGURE 4. IGM 11463, holotype of Vaquerosella perrillatae sp. nov. A, aboral side. B, oral side. C, posterior side. D, left lateral side.
Fig. 2. Sinohippus sampelayoi, IGME 1175M in Presence of the Asian horse Sinohippus in the Miocene of Europe
Fig. 2. Sinohippus sampelayoi, IGME 1175M, holotype. Fragment of right hemimandible with p2, d2, p3, d3, p4, d4, m1, m2, and m3. In occlusal (A), buccal (B), and lingual (C) views.
FIG. 8. Mongolemys elegans, additional material. IGM 90 in New material of Mongolemys elegans Khosatzky and Mlynarski, 1971 (Testudines: Lindholmemydidae), from the Late Cretaceous of Mongolia with comments on bone histology and phylogeny
FIG. 8. Mongolemys elegans, additional material. IGM 90/30, small articulated shell: A–B, dorsal view; C–D, ventral view. IGM 90/22–23, one juvenile and one hatchling associated shells: E–F, dorsal view. IGM 90/31, nearly complete plastron of a juvenile: G–H, ventral view. IGM 90/51, complete carapace and caudal vertebrae series: I–J, ventral view. IGM 90/54, partial carapace showing the complete series of thoracic vertebrae: K–L, ventral view. IGM 90/41, complete right hyoplastron from a juvenile specimen: M, ventral view; N, dorsal view. Abbreviations: abs, axillary buttress scar; brg, bridge; cav, caudal vertebra. (See fig. 4 for remaining abbreviations).
FIG. 4. Mongolemys elegans IGM 90 in New material of Mongolemys elegans Khosatzky and Mlynarski, 1971 (Testudines: Lindholmemydidae), from the Late Cretaceous of Mongolia with comments on bone histology and phylogeny
FIG. 4. Mongolemys elegans IGM 90/55, partially preserved skull. A–B, ventral view; C–D, dorsal view. Abbreviations in addition to those in figures 2 and 3: fbs, foramen caroticum basiphenoidale.
FIG. 6. Mongolemys elegans paratype IGM 90 in New material of Mongolemys elegans Khosatzky and Mlynarski, 1971 (Testudines: Lindholmemydidae), from the Late Cretaceous of Mongolia with comments on bone histology and phylogeny
FIG. 6. Mongolemys elegans paratype IGM 90/11, long bones. Left femur: A, ventral view; B, posterior. Right humerus: C, ventral view; D, dorsal view. Left tibia: E, dorsal view; F, ventral view. Left fibula: G, dorsal view; H, ventral view.
FIG. 2. Mongolemys elegans paratype IGM 90 in New material of Mongolemys elegans Khosatzky and Mlynarski, 1971 (Testudines: Lindholmemydidae), from the Late Cretaceous of Mongolia with comments on bone histology and phylogeny
FIG. 2. Mongolemys elegans paratype IGM 90/11, skull (cranium and lower jaw): A–B, dorsal view; C–D, ventrolateral view, removing the left ramus; E–F, ventral view, with the left ramus in place; G–H, lateral view; I–J, medial view of the left ramus and quadrate. Abbreviations: an, angular; ar, articular; bs, basisphenoid; cor, coronoid; den, dentary; fpc, foramen posterius canalis carotici; fr, frontal; fst, foramen stapedius temporalis; ju, jugal; mx, maxilla; pa, parietal; pf, prefrontal; pmx, premaxilla; po, postorbital; ppe, processus pterygoideus externus; pra, prearticular; pt, pterygoid; qu, quadrate; sa, surangular; scm, sulcus cartilaginous meckelii.
FIG. 5. Mongolemys elegans paratype IGM 90 in New material of Mongolemys elegans Khosatzky and Mlynarski, 1971 (Testudines: Lindholmemydidae), from the Late Cretaceous of Mongolia with comments on bone histology and phylogeny
FIG. 5. Mongolemys elegans paratype IGM 90/11, articulated shell (carapace and plastron): A–B, carapace, dorsal view; C–D, carapace, ventral view; E–F, plastron, ventral view; G–H, plastron, dorsal view. Abbreviations: abd, abdominal scale; anl, anal scale; axb, axillary buttress; c, costal; ce, cervical scale; en, entoplastron; ep, epiplastron; fem, femoral scale; gul, gular scale; hum, humeral scale, hyo, hyoplastron; hyp, hypoplastron; if, inframarginal scale; ing, inguinal buttress; isc, ischium; lpp, anal scale m, marginal scale; n, neural; p, peripheral; pl, pleural scale; pub, pubis; py, pygal scale; s, suprapygal scale, v, vertebral scale; xip, xiphiplastron. Missing portions of bone in black, scales in dotted lines. Labels in bold indicate scales.
FIG. 3. Mongolemys elegans paratype IGM 90 in New material of Mongolemys elegans Khosatzky and Mlynarski, 1971 (Testudines: Lindholmemydidae), from the Late Cretaceous of Mongolia with comments on bone histology and phylogeny
FIG. 3. Mongolemys elegans paratype IGM 90/11, isolated left otic chamber-quadrate: A–B, anterior view; C–D, medial view; E–F, posterior view. Abbreviations: ex, exoccipital; faf, fossa acustico-facialis; fnt, foramen nervi trigemini; ha, hiatus acusticus; op, opisthotic; pr, prootic; qu, quadrate; sa, surangular; scm, sulcus cartilaginous meckelii; so, supraoccipital; sq, squamosal.
Fig. 4. Zangerlia ukhaachelys, IGM 90 in Zangerlia ukhaachelys, New Species, a Nanhsiungchelyid Turtle from the Late Cretaceous of Ukhaa Tolgod, Mongolia
Fig. 4. Zangerlia ukhaachelys, IGM 90/1, holotype, Upper Cretaceous of Mongolia. Ventral view of plastron. Abbreviations: AB, abdominal scute; AN, anal scute; ent, entoplastron; epi, epiplastron; FE, femoral scute; HU, humeral scute; hyo, hyoplastron; hyp, hypoplastron; IM, inframarginal scute; PE, pectoral scute; per, peripheral; xi, xiphiplastron.
Fig. 3. Zangerlia ukhaachelys, IGM 90 in Zangerlia ukhaachelys, New Species, a Nanhsiungchelyid Turtle from the Late Cretaceous of Ukhaa Tolgod, Mongolia
Fig. 3. Zangerlia ukhaachelys, IGM 90/1, holotype, Upper Cretaceous of Mongolia. Ventral view of plastron.
Fig. 1. Zangerlia ukhaachelys. IGM 90 in Zangerlia ukhaachelys, New Species, a Nanhsiungchelyid Turtle from the Late Cretaceous of Ukhaa Tolgod, Mongolia
Fig. 1. Zangerlia ukhaachelys. IGM 90/1, holotype, Upper Cretaceous of Mongolia. Photographs were manipulated digitally to enhance sutures. A, Oblique dorsal view of mandible; B, dorsal view of mandible; C, dorsal view of cranium; D, ventral view of cranium. Abbreviations: desc proc, descending process of frontal; ex, exoccipital; fr, frontal; mx, maxilla; op, opisthotic; pa, parietal; pf, prefrontal; pm, premaxilla; po, postorbital; pro, prootic; qu, quadrate; rec lab op, recessus labyrinthicus opisthoticus; rec lab pro, recessus labyrinthicus prooticus; so, supraoccipital; vo, vomer;?, bone of uncertain homology.
Fig. 2. Pinacosaurus grangeri. IGM 100 in A New Specimen of Pinacosaurus grangeri (Dinosauria: Ornithischia) from the Late Cretaceous of Mongolia: Ontogeny and Phylogeny of Ankylosaurs
Fig. 2. Pinacosaurus grangeri. IGM 100/1014. Dorsal view of skull. See appendix 4 for abbreviations. Scale bar equals 5 cm.
Fig. 4. Pinacosaurus grangeri. IGM 100 in A New Specimen of Pinacosaurus grangeri (Dinosauria: Ornithischia) from the Late Cretaceous of Mongolia: Ontogeny and Phylogeny of Ankylosaurs
Fig. 4. Pinacosaurus grangeri. IGM 100/1014. Stereopairs of narial region in left anterolateral view showing narial apertures and recesses. See appendix 4 for abbreviations. Scale bar equals 2 cm.
Fig. 8. Pinacosaurus grangeri. IGM 100 in A New Specimen of Pinacosaurus grangeri (Dinosauria: Ornithischia) from the Late Cretaceous of Mongolia: Ontogeny and Phylogeny of Ankylosaurs
Fig. 8. Pinacosaurus grangeri. IGM 100/1014. Left hemimandible in buccal (A) and lingual (B) views. See appendix 4 for abbreviations. Scale bar equals 5 cm.
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