The Oregon Explorer Experience: An Internship with a Statewide Geospatial Atlas

The Professional Science Master’s program requires all graduates to complete an internship and prepare a descriptive report in lieu of a master’s thesis. In 2009 I concluded a three-month full-time internship with the Institute for Natural Resources (INR). Oregon Explorer (OE) is a collaborative effort between INR and Oregon State University Libraries (OSUL); OE is a web-based digital library that provides information and geospatial data for the state of Oregon to natural resource decision-makers and practitioners. I worked as a geographical information systems (GIS) intern for Oregon Explorer. Developing and completing this internship, which focused on addressing a public need, provided me an opportunity to learn techniques such as business and communication skills, applications like ERDAS and Adobe Creative Suite 2, and software languages such as HyperText Markup Language (HTML), ArcIMS AXL, and Extensible Markup Language (XML). This report discusses my internship’s scientific, ethical, and financial relevance as required by PSM degree guidelines. Additional background information is provided on the development of GIS, the ethical implications of web-based geospatial information, emerging technologies associated with building and maintaining on-line media for the public, and other benefits I gained from my internship with Oregon Explorer.Keywords: spatial data, PSM, Professional Science Master's, Digital Library, BitTorrent, Oregon Explore

NMR characterization of spin-1/2 alternating antiferromagnetic chains in the high-pressure phase of (VO)2P2O7

Local-susceptibility measurements via the NMR shifts of $^{31}$P and $^{51}$V nuclei in the high-pressure phase of (VO)$_{2}$P$_{2}$O$_{7}$ confirmed the existence of a unique alternating antiferromagnetic chain with a zero-field spin gap of 34 K. The $^{31}$P nuclear spin-lattice relaxation rate scales with the uniform spin susceptibility below about 15 K which shows that the temperature dependence of both the static and dynamical spin susceptibilities becomes identical at temperatures not far below the spin-gap energy.Comment: 6 pages, 5 figures; To be published in J. Phys. Condens. Matte

Formation of Sub-galactic Clouds under UV Background Radiation

The effects of the UV background radiation on the formation of sub-galactic clouds are studied by means of one-dimensional hydrodynamical simulations. The radiative transfer of the ionizing photons due to the absorption by HI, HeI and HeII, neglecting the emission, is explicitly taken into account. We find that the complete suppression of collapse occurs for the clouds with circular velocities typically in the range V_c \sim 15-40 km/s and the 50% reduction in the cooled gas mass with V_c \sim 20-55 km/s. These values depend most sensitively on the collapse epoch of the cloud, the shape of the UV spectrum, and the evolution of the UV intensity. Compared to the optically thin case, previously investigated by Thoul & Weinberg (1996), the absorption of the external UV photon by the intervening medium systematically lowers the above threshold values by \Delta V_c \sim 5 km/s. Whether the gas can contract or keeps expanding is roughly determined by the balance between the gravitational force and the thermal pressure gradient when it is maximally exposed to the external UV flux. Based on our simulation results, we discuss a number of implications on galaxy formation, cosmic star formation history, and the observations of quasar absorption lines. In Appendix, we derive analytical formulae for the photoionization coefficients and heating rates, which incorporate the frequency/direction-dependent transfer of external photons.Comment: 38 pages, 16 figures, accepted for publication in Ap

Thermotomaculum hydrothermale gen. nov., sp. nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough

http://www.godac.jamstec.go.jp/darwin/cruise/natsushima/nt08-13/

Modifying the surface electronic properties of YBa2Cu3O7-delta with cryogenic scanning probe microscopy

We report the results of a cryogenic study of the modification of YBa2Cu3O7-delta surface electronic properties with the probe of a scanning tunneling microscope (STM). A negative voltage applied to the sample during STM tunneling is found to modify locally the conductance of the native degraded surface layer. When the degraded layer is removed by etching, the effect disappears. An additional surface effect is identified using Scanning Kelvin Probe Microscopy in combination with STM. We observe reversible surface charging for both etched and unetched samples, indicating the presence of a defect layer even on a surface never exposed to air.Comment: 6 pages, 4 figures. To appear in Superconductor Science and Technolog

Metagenomics reveals our incomplete knowledge of global diversity

Financial support was provided by projects BFU2006-06003 from the Spanish Ministry of Education and Science (MEC) and GV/2007/050 from the Generalitat Valenciana, Spain. J.T. is a recipient of a contract in the FIS Program from ISCIII, Spanish Ministry of Health.Pignatelli, M.; Aparicio Pla, G.; Blanquer Espert, I.; Hernández García, V.; Moya, A.; Tamames, J. (2008). Metagenomics reveals our incomplete knowledge of global diversity. Bioinformatics. 24(18):2124-2125. https://doi.org/10.1093/bioinformatics/btn355S212421252418Koski, L. B., & Golding, G. B. (2001). The Closest BLAST Hit Is Often Not the Nearest Neighbor. Journal of Molecular Evolution, 52(6), 540-542. doi:10.1007/s002390010184Krause, L., Diaz, N. N., Goesmann, A., Kelley, S., Nattkemper, T. W., Rohwer, F., … Stoye, J. (2008). Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research, 36(7), 2230-2239. doi:10.1093/nar/gkn038Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., McHardy, A. C., … Kyrpides, N. C. (2007). Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods, 4(6), 495-500. doi:10.1038/nmeth1043Tamames, J., & Moya, A. (2008). Estimating the extent of horizontal gene transfer in metagenomic sequences. BMC Genomics, 9(1), 136. doi:10.1186/1471-2164-9-136Tringe, S. G. (2005). Comparative Metagenomics of Microbial Communities. Science, 308(5721), 554-557. doi:10.1126/science.1107851Tringe, S. G., Zhang, T., Liu, X., Yu, Y., Lee, W. H., Yap, J., … Ruan, Y. (2008). The Airborne Metagenome in an Indoor Urban Environment. PLoS ONE, 3(4), e1862. doi:10.1371/journal.pone.0001862COLE, F. N. (1900). AMERICAN MATHEMATICAL SOCIETY. Science, 11(263), 66-67. doi:10.1126/science.11.263.6

A fresh look at the evolution and diversification of photochemical reaction centers

In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers

Diversity of Francisella Species in Environmental Samples from Martha’s Vineyard, Massachusetts

We determined whether Francisella spp. are present in water, sediment, and soil from an active tularemia natural focus on Martha’s Vineyard, Massachusetts, during a multiyear outbreak of pneumonic tularemia. Environmental samples were tested by polymerase chain reaction (PCR) targeting Francisella species 16S rRNA gene and succinate dehydrogenase A (sdhA) sequences; evidence of the agent of tularemia was sought by amplification of Francisella tularensis-specific sequences for the insertion element ISFTu2, 17-kDa protein gene tul4, and the 43-kDa outer membrane protein gene fopA. Evidence of F. tularensis subsp. tularensis, the causative agent of the human infections in this outbreak, was not detected from environmental samples despite its active transmission among ticks and animals in the sampling site. Francisella philomiragia was frequently detected from a brackish-water pond using Francisella species PCR targets, and subsequently F. philomiragia was isolated from an individual brackish-water sample. Distinct Francisella sp. sequences that are closely related to F. tularensis and Francisella novicida were detected from samples collected from the brackish-water pond. We conclude that diverse Francisella spp. are present in the environment where human cases of pneumonic tularemia occur

Tony Blair and John Howard: comparative predominance and 'Institution Stretch' in the UK and Australia

It has recently been argued that the UK premier enjoys a level of executive power unavailable to US presidents, but how does he or she compare to another prime minister operating within a broadly similar system? Commonalities of intra-executive influence and capacity exist under the premierships in the UK and Australia. Discrete institutional constraints and deviations are evident, but trends and similarities in resource capacity can be clearly identified. These include: the growth of the leaders' office; broadening and centralising of policy advice and media operations; and strengthening of the role and function of ministerial advisers. I contend that this amounts to 'institution stretch', with new structures, processes and practices becoming embedded in the political system by the incumbents. © 2007 The Author. Journal compilation © 2007 Political Studies Association