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  • 1
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    Estimating surface roughness of terrestrial laser scan data using orthogonal distance regression (2011)
    Geological Society of America (GSA)
    Details
    Publication Date: 2011-07-01
    Description: With the increasing accessibility of terrestrial light detection and ranging scanners (LiDAR), generating tools to elicit meaningful information from high-density point cloud data has become of paramount importance. Surface roughness is one metric that has gained popularity, largely due to the accuracy and density of LiDAR-derived point cloud data. Surface roughness is typically defined as a spread of point distances from a reference datum, the standard deviation of point distances from a model surface being a commonly employed model. Unfortunately, a recent literature review has found that existing surface roughness models are far from standardized and may be prone to error resulting from underlying surface topography. In the research presented here, we develop a surface roughness model that is robust to underlying topographic variability by segmenting the point cloud with a three-dimensional regular grid, establishing local (grid cell) reference planes by orthogonal distance regression, and estimating the surface roughness of each grid cell as the standard deviation of orthogonal point-to-plane distances. This surface roughness model is employed to identify fracture and rubble zone distributions within a terrestrial LiDAR scan from a basalt outcrop in southeast Idaho, and the results are compared to a more common model based on ordinary least-squares plane fitting. Results indicate that the orthogonal regression model is robust to outcrop orientation and that the ordinary least-squares model systematically overestimates surface roughness by contaminating estimates with spatially correlated errors that increase with decreasing grid size.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 2
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    Experimental evaluation of terrestrial LiDAR-based surface roughness estimates (2012)
    Geological Society of America (GSA)
    Details
    Publication Date: 2012-02-01
    Description: The rapid proliferation of portable, ground-based light detection and ranging (LiDAR) instruments suggests the need for additional quantitative tools complementary to the commonly invoked digital terrain model (DTM). One such metric is surface roughness, which is a measure of local-scale topographic variability and has been shown to be effective for mapping discrete morphometric features, i.e., fractures in outcrop, landslide scarps, and alluvial fan deposits, to name a few. Several surface roughness models have been proposed, the most common of which is based on the standard deviation of point distances from a reference datum, e.g., DTM panels or best-fit planes. In the present work, we evaluate the accuracy of these types of surface roughness models experimentally by constructing a surface of known roughness, acquiring terrestrial LiDAR scans of the surface at 25 dual-axis rotations, and comparing surface roughness estimates for each rotation calculated by three surface roughness models. Results indicate that a recently proposed surface roughness model based on orthogonal distance regression (ODR) planes and orthogonal point-to-plane distance measurements is generally preferred on the basis of minimum error surface roughness estimates. In addition, the effects of terrestrial LiDAR sampling errors are discussed with respect to this ODR-based surface roughness model, and several practical suggestions are made for minimizing these effects. These include (1) positioning the laser scanner at the largest reasonable distance from the scanned surface, (2) maintaining half-angles for individual scans at less than 22.5°, and (3) minimizing occlusion (shadowing) errors by using multiple, merged scans with the least possible overlap.
    Electronic ISSN: 1553-040X
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 3
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    Analyses of pig genomes provide insight into porcine demography and evolution (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-11-16
    Description: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Groenen, Martien A M -- Archibald, Alan L -- Uenishi, Hirohide -- Tuggle, Christopher K -- Takeuchi, Yasuhiro -- Rothschild, Max F -- Rogel-Gaillard, Claire -- Park, Chankyu -- Milan, Denis -- Megens, Hendrik-Jan -- Li, Shengting -- Larkin, Denis M -- Kim, Heebal -- Frantz, Laurent A F -- Caccamo, Mario -- Ahn, Hyeonju -- Aken, Bronwen L -- Anselmo, Anna -- Anthon, Christian -- Auvil, Loretta -- Badaoui, Bouabid -- Beattie, Craig W -- Bendixen, Christian -- Berman, Daniel -- Blecha, Frank -- Blomberg, Jonas -- Bolund, Lars -- Bosse, Mirte -- Botti, Sara -- Bujie, Zhan -- Bystrom, Megan -- Capitanu, Boris -- Carvalho-Silva, Denise -- Chardon, Patrick -- Chen, Celine -- Cheng, Ryan -- Choi, Sang-Haeng -- Chow, William -- Clark, Richard C -- Clee, Christopher -- Crooijmans, Richard P M A -- Dawson, Harry D -- Dehais, Patrice -- De Sapio, Fioravante -- Dibbits, Bert -- Drou, Nizar -- Du, Zhi-Qiang -- Eversole, Kellye -- Fadista, Joao -- Fairley, Susan -- Faraut, Thomas -- Faulkner, Geoffrey J -- Fowler, Katie E -- Fredholm, Merete -- Fritz, Eric -- Gilbert, James G R -- Giuffra, Elisabetta -- Gorodkin, Jan -- Griffin, Darren K -- Harrow, Jennifer L -- Hayward, Alexander -- Howe, Kerstin -- Hu, Zhi-Liang -- Humphray, Sean J -- Hunt, Toby -- Hornshoj, Henrik -- Jeon, Jin-Tae -- Jern, Patric -- Jones, Matthew -- Jurka, Jerzy -- Kanamori, Hiroyuki -- Kapetanovic, Ronan -- Kim, Jaebum -- Kim, Jae-Hwan -- Kim, Kyu-Won -- Kim, Tae-Hun -- Larson, Greger -- Lee, Kyooyeol -- Lee, Kyung-Tai -- Leggett, Richard -- Lewin, Harris A -- Li, Yingrui -- Liu, Wansheng -- Loveland, Jane E -- Lu, Yao -- Lunney, Joan K -- Ma, Jian -- Madsen, Ole -- Mann, Katherine -- Matthews, Lucy -- McLaren, Stuart -- Morozumi, Takeya -- Murtaugh, Michael P -- Narayan, Jitendra -- Nguyen, Dinh Truong -- Ni, Peixiang -- Oh, Song-Jung -- Onteru, Suneel -- Panitz, Frank -- Park, Eung-Woo -- Park, Hong-Seog -- Pascal, Geraldine -- Paudel, Yogesh -- Perez-Enciso, Miguel -- Ramirez-Gonzalez, Ricardo -- Reecy, James M -- Rodriguez-Zas, Sandra -- Rohrer, Gary A -- Rund, Lauretta -- Sang, Yongming -- Schachtschneider, Kyle -- Schraiber, Joshua G -- Schwartz, John -- Scobie, Linda -- Scott, Carol -- Searle, Stephen -- Servin, Bertrand -- Southey, Bruce R -- Sperber, Goran -- Stadler, Peter -- Sweedler, Jonathan V -- Tafer, Hakim -- Thomsen, Bo -- Wali, Rashmi -- Wang, Jian -- Wang, Jun -- White, Simon -- Xu, Xun -- Yerle, Martine -- Zhang, Guojie -- Zhang, Jianguo -- Zhang, Jie -- Zhao, Shuhong -- Rogers, Jane -- Churcher, Carol -- Schook, Lawrence B -- 095908/Wellcome Trust/United Kingdom -- 249894/European Research Council/International -- 5 P41 LM006252/LM/NLM NIH HHS/ -- 5 P41LM006252/LM/NLM NIH HHS/ -- BB/E010520/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010520/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010768/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E011640/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G004013/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H005935/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/I025328/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0900950/Medical Research Council/United Kingdom -- P20-RR017686/RR/NCRR NIH HHS/ -- P30 DA018310/DA/NIDA NIH HHS/ -- R13 RR020283A/RR/NCRR NIH HHS/ -- R13 RR032267A/RR/NCRR NIH HHS/ -- R21 DA027548/DA/NIDA NIH HHS/ -- R21 HG006464/HG/NHGRI NIH HHS/ -- T32 AI083196/AI/NIAID NIH HHS/ -- England -- Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands. martien.groenen@wur.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23151582" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Demography ; Genome/*genetics ; Models, Animal ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Sus scrofa/*classification/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Energy storage: Power revolution (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-10-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fairley, Peter -- England -- Nature. 2015 Oct 29;526(7575):S102-4. doi: 10.1038/526S102a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26509948" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Introduction: Next generation biofuels (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-06-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fairley, Peter -- England -- Nature. 2011 Jun 22;474(7352):S2-5. doi: 10.1038/474S02a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21697838" target="_blank"〉PubMed〈/a〉
    Keywords: *Biofuels/economics/supply & distribution/utilization ; Biomass ; Conservation of Natural Resources/*methods/*trends ; Global Warming/prevention & control ; Waste Management/methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    The origin of radon anomalies along normal faults in an active rift and geothermal area (2016)
    Geological Society of America (GSA)
    In: Geosphere
    Details
    Publication Date: 2016-10-08
    Description: Radon anomalies are widely reported in the vicinity of active faults, where they are often inferred to result from upward migration of fluids along fault zones. We examine the up-fault flow hypothesis by measuring radon ( 220 Rn and 222 Rn) in soil gas above two active normal fault zones within the central Taupo rift, New Zealand. In agreement with previous investigations, we find that the average concentrations of both radon isotopes are generally higher near mapped faults, although in some cases we find that the difference with background populations is not significant. Soil samples recovered from 1 m depth indicate that some of the radon anomalies along faults may reflect local changes in soil types. The 220 Rn isotope emanation measured from extracted soil samples shows a linear correlation with the field concentration measurements (R 2 = 0.90, p value = 3 x 10 –6 ), whereas 222 Rn emanation shows no linear correlation (R 2 = 0.17, p value = 0.17). The soil gas isotopes measured show a significant linear correlation of 220 Rn and 222 Rn concentrations (R 2 = 0.44–0.55, p value 〈10 –5 ) near faults. This correlation suggests a constant radon isotopic ratio is emitted from the soils tested, and this finding is supported by emission data measured on extracted soil samples. The distribution of 222 Rn concentration compared to 220 Rn can be explained by small-scale diffusion for 〉90% of the soil gas measurements, showing that a majority of radon anomalies along faults are not necessarily caused by advection of gases along fault planes and can be explained by an increase in radon soil emanation. However, diffusion cannot account for all of the observed patterns in the data, and in some specific locations along faults, 222 Rn concentrations are most likely produced by advective flow of subsurface gases, suggesting channelized gas flow in portions of some faults.
    Electronic ISSN: 1553-040X
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 7
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    The genome of a songbird (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-04-03
    Description: The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187626/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187626/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warren, Wesley C -- Clayton, David F -- Ellegren, Hans -- Arnold, Arthur P -- Hillier, Ladeana W -- Kunstner, Axel -- Searle, Steve -- White, Simon -- Vilella, Albert J -- Fairley, Susan -- Heger, Andreas -- Kong, Lesheng -- Ponting, Chris P -- Jarvis, Erich D -- Mello, Claudio V -- Minx, Pat -- Lovell, Peter -- Velho, Tarciso A F -- Ferris, Margaret -- Balakrishnan, Christopher N -- Sinha, Saurabh -- Blatti, Charles -- London, Sarah E -- Li, Yun -- Lin, Ya-Chi -- George, Julia -- Sweedler, Jonathan -- Southey, Bruce -- Gunaratne, Preethi -- Watson, Michael -- Nam, Kiwoong -- Backstrom, Niclas -- Smeds, Linnea -- Nabholz, Benoit -- Itoh, Yuichiro -- Whitney, Osceola -- Pfenning, Andreas R -- Howard, Jason -- Volker, Martin -- Skinner, Bejamin M -- Griffin, Darren K -- Ye, Liang -- McLaren, William M -- Flicek, Paul -- Quesada, Victor -- Velasco, Gloria -- Lopez-Otin, Carlos -- Puente, Xose S -- Olender, Tsviya -- Lancet, Doron -- Smit, Arian F A -- Hubley, Robert -- Konkel, Miriam K -- Walker, Jerilyn A -- Batzer, Mark A -- Gu, Wanjun -- Pollock, David D -- Chen, Lin -- Cheng, Ze -- Eichler, Evan E -- Stapley, Jessica -- Slate, Jon -- Ekblom, Robert -- Birkhead, Tim -- Burke, Terry -- Burt, David -- Scharff, Constance -- Adam, Iris -- Richard, Hugues -- Sultan, Marc -- Soldatov, Alexey -- Lehrach, Hans -- Edwards, Scott V -- Yang, Shiaw-Pyng -- Li, Xiaoching -- Graves, Tina -- Fulton, Lucinda -- Nelson, Joanne -- Chinwalla, Asif -- Hou, Shunfeng -- Mardis, Elaine R -- Wilson, Richard K -- BB/D013704/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010652/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F007590/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBE0175091/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/E/I/00001425/Biotechnology and Biological Sciences Research Council/United Kingdom -- MC_U137761446/Medical Research Council/United Kingdom -- P30 DA018310/DA/NIDA NIH HHS/ -- R01 DC007218/DC/NIDCD NIH HHS/ -- R01 GM059290/GM/NIGMS NIH HHS/ -- R01 GM085233/GM/NIGMS NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- R01 NS045264/NS/NINDS NIH HHS/ -- R01NS051820/NS/NINDS NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Apr 1;464(7289):757-62. doi: 10.1038/nature08819.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. wwarren@watson.wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360741" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/genetics ; Animals ; Auditory Perception/genetics ; Brain/physiology ; Chickens/genetics ; Evolution, Molecular ; Female ; Finches/*genetics/physiology ; Gene Duplication ; Gene Regulatory Networks/genetics ; Genome/*genetics ; Male ; MicroRNAs/genetics ; Models, Animal ; Multigene Family/genetics ; Retroelements/genetics ; Sex Chromosomes/genetics ; Terminal Repeat Sequences/genetics ; Transcription, Genetic/genetics ; Vocalization, Animal/physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Physical constraints on geologic CO2 sequestration in low-volume basalt formations (2014)
    Geological Society of America (GSA)
    Details
    Publication Date: 2014-02-27
    Description: Deep basalt formations within large igneous provinces have been proposed as target reservoirs for carbon capture and sequestration on the basis of favorable CO 2 -water-rock reaction kinetics that suggest carbonate mineralization rates on the order of 10 2 –10 3 d. Although these results are encouraging, there exists much uncertainty surrounding the influence of fracture-controlled reservoir heterogeneity on commercial-scale CO 2 injections in basalt formations. This work investigates the physical response of a low-volume basalt reservoir to commercial-scale CO 2 injections using a Monte Carlo numerical modeling experiment such that model variability is solely a function of spatially distributed reservoir heterogeneity. Fifty equally probable reservoirs are simulated using properties inferred from the deep eastern Snake River Plain aquifer in southeast Idaho, and CO 2 injections are modeled within each reservoir for 20 yr at a constant mass rate of 21.6 kg s –1 . Results from this work suggest that (1) formation injectivity is generally favorable, although injection pressures in excess of the fracture gradient were observed in 4% of the simulations; (2) for an extensional stress regime (as exists within the eastern Snake River Plain), shear failure is theoretically possible for optimally oriented fractures if S h ≤ 0.70S V ; and (3) low-volume basalt reservoirs exhibit sufficient CO 2 confinement potential over a 20 yr injection program to accommodate mineral trapping rates suggested in the literature.
    Print ISSN: 0016-7606
    Electronic ISSN: 1943-2674
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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