User:Dcrjsr

Dcrjsr is a user created by Jane Shelby Richardson at Duke University. This user page is mainly intended as a way to help organize the uploaded images.

Small galleries are on this page, while larger ones are linked - such as those for Protein ribbon drawings or High Sierra landscapes, or Sierra Nevada flowers.

One section pertains to structural bioinfomatics: ribbon drawings of 3D protein and RNA structures, illustrations of aspects of crystallographic or NMR models and methodology, and examples of structural motifs. More background information can be found at our lab web site. I am the organizer, and a participant, in WikiProject Biophysics

The second section includes images of landscapes, flowers, and animals - mostly photographed in the Sierra Nevada mountains of California and mostly with geolocations. Note that I keep my camera set on Eastern US time zone, so the metadata does not show local time if taken elsewhere.

• Dcrjsr/POTD, featured, quality, & valued images
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  TIM ribbon - en:wikipedia Picture of Day 091119
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  TIM ribbon pastel - featured image on Commons
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  1GWE antiparallel beta sheet - valued image on Commons
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  Ranger's buttons - quality image on Commons
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  Sierra arctic gentians (Gentiana newberryi var. tiogana) - valued image
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  Banner Peak & 1000-Island Lake - valued image on Commons

Section on Protein and Nucleic Acid Structures

Click here for the gallery of Dcrjsr/Protein Ribbon Drawings

Example protein ribbon drawing: CuZn SOD

• Dcrjsr/Protein Structure Detail images
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  CuZn SOD active site
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  Contacts between RNAse and U vanadate inhibitor
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  Selectivity region of K+ channel, from 1bl8
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  GCN4 Leu-zip hydrophobic core, with Asn (2zta)
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  Collagen Gly-Pro-hyPro triple helix (1cag)
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  Phi-Psi-Omega backbone dihedral angles
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  PhiPsi diagram with plane and labels
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  Alpha vs 310 helix end views
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  Helical wheel diagram of alpha helix
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  Wenxiang diagram of alpha helix
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  Antiparallel beta sheet from 1GWE, face & edge views
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  Classic beta-bulge schematic
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  Right-handed vs left-handed crossovers

• Dcrjsr/Protein Crystallography images
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  Asymmetric Staph nuclease crystals
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  CuZn SOD precession photo
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  Staph nuclease brass model to UV worm
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  Staph nuclease Arg-Phe on glass map stack
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  Helix in high-resolution electron density
• Ultra-high resolution electron density: crambin P41, 3nir
  Ultra-high resolution electron density: crambin P41, 3nir
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  Hydrogens in protein electron density
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  4fc1 Arg17 neutron H vs D in map
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  Modeling alternate conformers in KiNG

• Dcrjsr/Structure Validation images
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  Structure validation concept
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  Incredulase: the model is not the molecule
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  Good all-atom contacts, 1gci Ala methyls
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  Low vs hi resolution hemoglobin detail
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  MolProbity Logo
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  Validation outlier legend, MolProbity
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  MolProbity clashscore vs year thru 2011
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  MolProbity validation outliers in 3D, on-line
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  27 lysine rotamers
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  Ramachandran plot, original 1963 outlines
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  1acx PCNA ProCheck Rama plot
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  Ramachandran plot for general amino acids
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  Ramachandran plot for Glycine
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  Ramachandran plot for Proline
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  Top8000 general-case Ramachandran plot
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  Glycine Ramachandran plot, Top8000
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  Top8000 trans Pro Ramachandran plot
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  Ramachandran redux, Gly, 3600x3600px
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  6 Ramachandran plots of wwPDB validation

• Dcrjsr/Protein Design images & audios
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  Betabellin model, early de novo design
• Betabellin sequence incantation
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  Felix model, early 4-helix bundle de novo design
• Felix sequence incantation
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  TOP7 protein design, structure confirmed (1qys)
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  PheA redesign template, gramicidin synthase

• Dcrjsr/3D Structure Prediction images
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  Target structure, with 354 predicted models (CASP8)
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  Cumulative plot of Calpha accuracy, CASP8 T0398

• Dcrjsr/RNA Structure images
• RNA backbone - suite vs residue
  RNA backbone - suite vs residue
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  RNA backbone - suite vs residue (tif format)
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  All-atom contacts for two GC base pairs of RNA
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  GNRA tetraloop motifs, 3 superimposed & annotated
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  S-motif in RNA, with backbone conformer labels
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  Kissing Loop motif (1zci), from GJKapral
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  tRNA Phe, from PDB 1ehz
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  G-riboswitch binding site: map, contacts, conformers
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  G riboswitch RNA, 1u8d
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  Tetrahymena Group I self-splicing intron, 1grz
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  Twort groupI intron, stereo ribbon
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  5S ribosomal RNA, ribbons
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  E coli 70S ribosome structure, QuteMol
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  Ecoli 70S ribosome pair w/ tRNA, mRNA
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  Ecoli 70S ribosome pair vs gentamicin drug
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  70S E coli ribosome outline
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  50S subunit archaeal ribosome, outline
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  RNA backbone rebuild 3cc2 5S 77

• Dcrjsr/DNA Structure images
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  Dickerson DNA dodecamer, from 1bna
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  Holliday junction DNA, from the protein complex in 2crx
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  Nucleosome DNA & histone structure, round, 1aoi
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  Nucleosome DNA and histone structure, 1aoi
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  Nucleosome DNA/protein complex, ribbon schematic
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  CAP protein dimer on bent DNA, 1cgp
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  Coiled-coil transcription factor Max, on DNA
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  Zn-finger transcription factor Zif268, on DNA
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  BmrR/DNA/TPP complex, untwisting the DNA
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  Clamp-loader, open clamp, & DNA, 3u5z

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• Dcrjsr/NMR Structure images
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  2k49 NMR ensemble ribbons
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  2k5d NMR ensemble ribbons
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  144 NMR models for ubiquitin, from PDB 2nr2
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  NH RDC target curves on NMRmodels, D58 in 1d3z

• Dcrjsr/WikiProject Biophysics images
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  Original Richards box photo, 1968
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  Institute of BioPhysics, Beijing
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  IISc Tata Auditorium entrance, Bangalore
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  Tata Auditorium, Indian Inst Science, Bangalore
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  King-Way Yau 2008 ARVO
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  Jane S Richardson B&W 2002
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  Irwin Fridovich in Duke office, 1994
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  Heads & neck of kinesin motor, Goodsell MotM 64
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  Topoisomerase Type I on DNA, Goodsell MotM 73
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  Topoisomerase II composite, Goodsell MotM 73
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  Clathrin cage & triskelion, Goodsell MotM 88
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  Cu,Zn superoxide dismutase (SOD) dimer, Goodsell MotM 94
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  Human Cu,Zn superoxide dismutase, Goodsell MotM 94
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  Mn and Fe SOD dimers, Goodsell MotM 94
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  Ni SOD hexamer, Goodsell MotM 94
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  Kai A,B,C circadian clock, Goodsell MotM 97
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  70S bacterial ribosome, small subunit front, Goodsell MotM 121
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  70S initiation, with Shine-Delgarno mRNA, Goodsell MotM 121
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  3 stages of elongation in 70S: EF-Tu, peptide, EF-G, Goodsell MotM 121
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  RF-1release factor in ribosome, Goodsell MotM 121
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  Antibiotics bound to 70S bacterial ribosome, Goodsell MotM 121
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  Aquaporin water-channel tetramer, Goodsell MotM 173
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  Seven colors of GFP-like proteins, Goodsell MotM 174
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  Tetramer of GFP-like dsRed from coral, Goodsell MotM 174
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  Apoptosome subunit & complex, Goodsell MotM 177
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  Apoptosomes of 3 species, Goodsell MotM 177
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  Cross-section of Ebolavirus, with proteins, Goodsell MotM 178
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  three Ebolavirus matrix proteins, Goodsell MotM 178
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  TAL effector protein bound to DNA, Goodsell MotM 180
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  TALE/nuclease/DNA engineered complex, Goodsell MotM 180
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  Cascade complex of Type I CRISPR, Goodsell MotM 181
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  Cas1,2,3 proteins of CRISPR, Goodsell MotM 181
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  Cas9 Cascade complex of Type III CRISPR, Goodsell MotM 181
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  Glucagon hormone bound to its receptor, Goodsell MotM 184
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  ALAD enzyme in lead poisoning, Goodsell MotM 196
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  Zika virus capsid, Goodsell MoTM 197
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  Zika virus cross-section on cell, Goodsell MoTM 197

Section on Landscapes, Plants, etc

Click here for the gallery of Dcrjsr/High Sierra landscape images, organized S to N by Wilderness area or Park

Example high Sierra image

Click here for the gallery of Dcrjsr/Eastern Sierra images

Example Eastern Sierra image

Click here for the gallery of Dcrjsr/Sierra Nevada flower images, organized by genus & species

Example flower image

Click here for the gallery of Dcrjsr/Death_Valley_superbloom_2016 images

Example superbloom image

Click here for the gallery of Dcrjsr/Sierra Nevada shrub images, organized by genus & species

Example shrub image

Click here for the gallery of Dcrjsr/Sierra Nevada tree images, organized by genus & species

Example tree image

Click here for the gallery of Dcrjsr/Duke Forest NC plant images

Example NC plant image

• Dcrjsr/Sedges, unidentified
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  Y-end sedge (Carex sp) close, Golden Lake
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  Y-end sedge (Carex sp) clump, Golden Lake
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  Round-end sedge close (Carex sp) Lake George
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  Round-end sedge (Carex sp) Lake George
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  Finger-end sedge close (Carex sp) Tioga
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  Finger-end sedge (Carex sp) by pond, Tioga
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  Large sedge (Carex sp) in edge of Lower Rock Creek
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  Large sedge close, Rock Creek Canyon
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  Large sedge (Carex sp) Rock Creek Canyon
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  Sedge (Carex sp) NW of Mono P (from BakerClaw)
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  Large sedge, seed head star, Oakland lawn
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  Unknown sedge (Carex), Tantalus Road, Oahu.]]

• Dcrjsr/Ferns & lower Gymnosperms
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  Equisetum arvense lining streambank, Aspendell
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  Equisetum arvense, sterile stem close
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  Green ephedra (Ephedra viridis) bush
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  Green ephedra (Ephedra viridis) close
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  Green ephedra, male cones & leaf scales

• Dcrjsr/Animal images
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  Gray fox, cameo
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  Gray fox, full-face
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  Gray fox, back twirl
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  Gray fox, over shoulder
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  Gray fox, sniff
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  Desert cottontail (Silvilagus audubonii) under sage bush
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  Desert cottontail (Silvilagus audubonii) back view
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  Desert cottontail (Silvilagus audubonii) front view
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  Desert cottontail (Silvilagus audubonii) side view
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  Blacktailed jackrabbit (Lepus californicus) Marin County
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  Pika in rocks, mouthful of dried grass
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  American pika (Ochotona princeps) camouflaged
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  Yellow-bellied marmot, near Kaweah Gap
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  Marmota flaviventris, on rock in meadow, 20-Lakes Basin
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  Marmota flaviventris standing, S of Donahue
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  Beldings ground squirrels (Spermophilus beldingi)
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  Chipmunk stuffing cheeks with seeds
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  Pack llamas posing, meadow N of Purple Lake
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  Bison classic profile, Yellowstone
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  Two bison at riverbend, Yellowstone
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  Two baby mule deer, Oakland CA
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  Mule deer buck full-face, Swall Mdws
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  Mule deer doe backlit, Swall Mdws
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  Striped skunk (Mephitis mephitis) Las Trampas
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  Black-headed grosbeak male, perched front
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  Black-headed grosbeak female, perched
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  Rufous hummingbird female, perched, front
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  Stellers jay perched on antelope brush
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  Purple finch, on gravel, front view
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  California quail male, on ceanothus bush
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  California quail chicks hiding by path
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  Great horned owl, closeup of mother and nestling
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  Green sea turtle (Chelonia mydas) onTurtle Beach Oahu
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  Green sea turtle (Chelonia mydas) looking around
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  Green sea turtle turning to leave the beach, Oahu
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  Green sea turtle heading back toward the sea, Turtle Beach
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  Green sea turtle partly wet by wave, heading seaward
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  Green sea turtle back in the water again, Turtle Beach
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  Orthoceras fossil cluster, black marine nautiloids

• Dcrjsr/Worldwide places images
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  Institute of BioPhysics, Beijing
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  Great Wall at Badaling, embrasure view
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  Great Wall at Badaling, view past tower
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  Gold lion in Forbidden City, Beijing
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  Hills in mist, Li River, China
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  "Big Temple" at Thanjavur, India
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  Temple elephant blessing, Thanjavur
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  Ramanujan museum, SASTRA, Kombakonam
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  Ramanujan statue, SASTRA, Kumbakonam
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  IISc Tata Auditorium entrance, Bangalore
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  Guest House entrance, IISc, Bangalore
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  Trees with pepper vines, Coorg, India
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  Green peppercorns (Piper nigrum) Coorg
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  Coffee tree (Caffea arabica) with berries
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  Small boat on river, Coorg, India
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  Wash day at riverbank, Coorg, India
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  View of green hillside, from clifftop in Orvieto Italy
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  Monastery hillside from clifftop in Orvieto Italy
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  Small tower across rooftops, Orvieto Italy
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  Wisteria in cobblestone cul-de-sac, Orvieto Italy
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  Narrow cobblestone street, Orvieto Italy
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  Old ladies in sun under arbor, Ostia Antica, Italy
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  Closeup of Roman road stones, Ostia Antica, Italy
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  Ancient Roman ampitheater, Ostia Antica, Italy
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  Monte Cofano from Erice, Sicily
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  Acanthus mollis flower spikes, Erice, Sicily
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  Elymian stone theatre, Segesta, Sicily
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  Gaudi iron door, LaPedrera, Barcelona
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  Tarragona Spain: sea view from Balcon terrace
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  Fireworks from the Balcon terrace, Tarragona Spain
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  Kings College, Cambridge UK

• Dcrjsr/US places images
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  Na Pali coast, Kauai - Hanakapi'ai Beach
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  Na Pali Coast profile, Kauai, from Kalalau Trail
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  Na Pali Coast, overlook of Kalalau Valley & cliffs
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  Large hole through island off La'ie Point, Oahu
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  View south from La'ie Point to Ka'a'awa, Oahu
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  Chinaman's Hat Island, off Ka'a'awa peninsula, Oahu
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  Diamond Head & Waikiki, from Tantalus Rd, Oahu
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  Marsh marigold bloom at edge of snowmelt WA
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  Marsh marigold (Caltha leptosepala)
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  Pacific Crest Trail in Washington woods
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  View SE from paved trail, Las Trampas
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  N along Rocky Ridge top, Las Trampas
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  California bay tree (U. californica) Las Trampas
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  View W into EBMUD watershed. Las Trampas
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  compressed-fossil rock, Las Trampas
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  Striped skunk (Mephitis mephitis) Las Trampas
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  Observation tower, Wildflower Center TX
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  Cafe & tower, Wildflower Center TX
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  Texas bluebonnet field (Lupinus texensis), with oaks
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  Path by bluebonnets, Wildflower Center TX
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  Bluebonnets by trail, Wildflower Center TX
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  Hedgehog cactus, Wildflower Center TX
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  Dragonfly sculpture, Wildflower Center TX
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  Great horned owl (Bubo virginianus) mother and nestling
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  Piney Mtn Road, Duke Forest, Durham NC
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  Concrete Bridge Rd N, dogwood branch
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  Concrete Bridge Rd S, starting downhill
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  View down from end of Piney Mtn Rd
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  Concrete Bridge, late summer, Duke Forest
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  New Hope Creek with blooming fringetree
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  New Hope Creek, Duke Forest, Durham NC
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  Duke Forest, misty morning woods
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  Moon thru branch tips, Duke Forest, Durham NC
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  Duke Forest seed pines after timbering
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  Sunderland Bridge, from Sugarloaf Mtn, MA
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  Town center of Sunderland, Massachusetts
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  Boulder on granite-slab shoulder, Welsh Mtn NH
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  Stone breakwater S of Saco River, Maine
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  Saco River harbor, Biddeford Maine

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ORCID: 0000-0002-3311-2944