Monthly Archives: April 2017

PNW EFR Website and database creation

From: Jessel, Tanner – FS
Sent: Thursday, April 27, 2017 5:32 PM
To: Youngblood, Anthony – FS < >; Burks, Matthew C -FS < >
Cc: Wilson, Todd – FS <twilson@fs.fed.us>
Subject: RE: PNW EFR Website and database creation

Hi Anthony,

I’m glad you pointed out the RNA site – I agree it is a good model. A less obvious feature buried in that site is an interactive map of all the NFS research natural areas available to scientists:

https://www.google.com/maps/d/viewer?t=h&msa=0&z=6&source=embed&ie=UTF8&mid=1P2E6FokQN4bYW8FvLqHr2ypmstk&ll=45.60095374529163%2C-120.3932115

Just a wild guess here as I don’t work on it – but could this be a useful feature for the Science Support Network on SharePoint? Perhaps a small database of research sites and opportunities in an Access Web App might be useful? I’m kind of getting the idea of a “matchmaking service” for PNW researchers and available research sites. I’m attaching a spreadsheet I created really quickly with the data from the OSU site for the locations specific to the forest service ( perhaps for no reason other than the RNA sites and the map interest me, and I want to have a handy reference back to it). Some ideas to expand the potential utility of a hypothetical “matchmaking” database might be to include other publications in TreeSearch done at the specific RNAs, and maybe the species available to study at the site. I’m not sure what that would end up looking like, but the idea interests me.

For the other part, I think you’ll be pleased to learn that Tiffany has built up a section for Experimental Forests and Ranges on the upcoming Drupal Site, and it is indeed modelled after RMRS:

https://zlpheweb003.phe.fs.fed.us/pnw_dev1/page/experimental-forests-and-ranges

Matt, the example content linked at http://www.fsl.orst.edu/chef/index.htm would make great content for an ESRI “Story Map” for our (ten?) experimental forests and ranges – the linked page http://www.fsl.orst.edu/chef/about2nd.htm really lends itself well to that medium.

All of the EF&R have really fascinating histories and research legacies that make for good stories.

-Tanner

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PNW-Research-Natural-Areas.xlsx

Online FS portal for data viz?

Hi Bob and Cheryl (also CC’ing Cindy with CAP and John with WO R&D as I think they may find this of interest):

Thank you both for the opportunity to learn about landscape visualization tools available to / from the Forest Service at last week’s conference on “Exploring Visualization Tools for Communicating Natural Resource Management Information” at PSU.

I wanted to follow up on a point I raised in the discussion of potential outcomes of the conference:

A barrier to Forest Service employees applying some of the available software tools may be that a “technical approval” is required to install non-standard software on Forest Service Machines. I’d mentioned perhaps the Forest Service could have non-standard software for landscape visualization and assessment hosted on the Forest Service’s Citrix Server Farm.

That would ideally lower the barrier to Forest Service managers to have the opportunity to easily “try out” some of the software tools available. A list of non-standard software already hosted on Citrix is available on SharePoint; I think it would be a great to see more software developed by the research stations hosted / available to try on the Citrix Farm.

Also – Taylor Mutch from CBI voiced a second idea to perhaps host Forest Service software on “Extreme Science and Engineering Discovery Environment” (XSEDE) platform for distributed / cloud computing and science applications. XSEDE offers the opportunity to develop “Science Gateways,” collections of domain-specific software and tools. “Science Gateways” are available here: https://portal.xsede.org/science-gateways. The closest examples to illustrate the concept applied to natural resource management are probably these two:

http://gateway.cigi.illinois.edu/home/

https://mygeohub.org/

This is beyond my area of expertise (I’m no software developer), but I had a thought that if PNW or the Forest Service in general had enough people with the skills to develop hosted versions of our desktop software applications, this could remove the impediment to Forest Service employees who might be intimidated by installing non-standard software on FS machines, and perhaps resolve a second issue of long-term disposition of software developed by Forest Service researchers.

As a new/temporary visitor to PNW, I was surprised to learn software is developed at PNW (and other research stations). I think it could be great addition to have some sort of online “science gateway” to gather these tools together, ideally with the option to try them out / run them online.

Thanks again,

Tanner

Tanner Jessel, MSIS
Science Communications Research Fellow
Forest Service

Pacific Northwest Research Station

p: 503-808-2108
f: 503-808-2130
1220 SW 3rd Ave, Suite 1400
Portland, OR 97207
www.fs.fed.us
Caring for the land and serving people

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Landscape Visualization Software

http://vterrain.org/Plants/Forestry/

Envision – A PNW product:

http://forsys.cfr.washington.edu/envision.html

https://www.fs.fed.us/t-d/programs/forest_mgmt/projects/landscapesim/envision.shtml

Not to be confused with:

http://envision.bioe.orst.edu/Downloads.aspx

Visual Nature Studio

http://3dnature.com/index.php/products/natureview/

VISualization of Terrestrial-Aquatic Systems (VISTAS).

http://blogs.evergreen.edu/vistas/

http://blogs.evergreen.edu/vistas/vistas-software/

Some more considered by the Forest Service here:

https://www.fs.fed.us/t-d/programs/forest_mgmt/projects/landscapesim/index.shtml

With a link out to http://vterrain.org/

https://sites.google.com/a/pdx.edu/dynamic-ecosystems-landscape-lab/research/landis-ii-development

http://www.landis-ii.org/

https://www.nrs.fs.fed.us/tools/landis/

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Steps to Access SharePoint via Drag+Drop Interface

Hi Matt,

From our chat yesterday:

https://support.microsoft.com/en-us/help/2629108/how-to-use-the-open-with-explorer-command-to-troubleshoot-issues-in-sharepoint-online

Example Document Library in Windows Explorer:

https://ems-team.usda.gov/sites/fs-rd-pnwwt/SitePages/Home.aspx

Click "Edit"

Then click "Library"

Then click a small icon, "Open With Explorer"

Hope this proves useful!

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PNW Quarterly Pubs

Hi Rhonda,

Here is what I came up with by way of instructions so far:

https://ems-team.usda.gov/sites/fs-rd-pnwcap/QuarterlyPubUpdate/Home.aspx

I have ten total tasks for the person to perform that gets you to the ability to generate a bibliography using whatever template you wish.

The attached spreadsheet could be used as something of a template to save a few steps.

I have a few screen captures of specific things that might benefit from illustration, but I’m not sure how to / if I want to include them.

This is a really interesting graphic here –

http://fsweb.wo.fs.fed.us/rd/images/adhoc/rits_components.jpg

Says “RITS can be used for accomplishment reporting.” It just seems really difficult to do accomplishment reporting if you can’t export data or sort it.

Got that here: here: http://fsweb.wo.fs.fed.us/rd/researchtools/rits/index.php

Do you want to sit down this week and go through the steps?

I keep thinking there has to be a better way than what I have come up with. I am curious to see if I can teach myself the computer coding that would allow us to do this a bit more elegantly in the 6 weeks I have left.

-Tanner

From: Jessel, Tanner – FS
Sent: Monday, April 17, 2017 5:26 PM
To: Mazza, Rhonda L -FS < >
Subject: FW: PNW Quarterly Pubs

Hi Rhonda,

I have been playing around with a few ideas on the process to get the data. Forwarded message is the output; immediately below are some notes about some issues encountered with the process to get to the output.

There have been some vexing problems with the project I should note a few of the issues encountered. A few notes below:

1. There are 178 items in my example

a. Visit “Product Search” (https://apps.fs.usda.gov/rnd/rits/searchProduct/productSearch)

b. Earliest Product_ID in my spreadsheet: 75826, entered on 09-12-2016

c. Latest Product_ID in my spreadsheet: 84135, entered on 02-28-2017

2. Of these, it is important to note that each item has a “Status” associated with it

a. 29 are “Approved” (I can’t tell what this means)

b. 1 is “Non-Treesearch” (a magazine article)

c. 1 is “Not yet Submitted for Review” (this is a 2016 publication)

d. 6 are “Pending Reviewer” (5 are “JRNL and 1 is GTR)

e. 140 are “Published to Web (I assume that this means “Published to TreeSearch”

3. It gets a bit interesting here…

a. I collected all of the digital object identifiers.

b. Not all of the items are from 2016

i. 1 – 1985

ii. 1 – 2005

iii. 1 – 2008

iv. 4- 2013

c. Maybe this does not matter if our goal is to communicate “New Items in TreeSearch This Quarter”

i. If the goal is only, “New items published in this quarter” then it does matter

4. I added the column “DOI” and grabbed this information from the TreeSearch XML – painfully, by hand.

a. 96 items have a DOI (most are journal articles; 3 are “Forest Service” GTR’s).

b. 29 items do not have a DOI

i. 11 “Miscellaneous”

ii. 2 Thesis

iii. 3 Book

iv. 6 JRNL

Apart from figuring out when things were actually published, here is where the DOI seems to have some bearing on the “semi-automated” component of the quarterly publication update reporting / e-mail update project.

I used the DOI to visit all of the online resources that had a doi (do this by combining http://doi.org/ with the actual doi).

· I collected each resource one-by-one to Mendeley Web by using the Mendeley Firefox Add-on

· I synced my Mendeley Web to Mendeley Desktop

Mendeley desktop has an interesting feature: it lets you view your collected items by journal.

That gave me an idea: how about grouping quarterly publications by journal?

I copied and pasted some examples below – you can see that the publications for the time range (September 2016 – March 2017) appear in a variety of journals.

I think this might be an approach that adds value for the reader over just an alpha list by author.

One thing I don’t like is there’s no link back to the TreeSearch publication. This could be manually added in, but that’s more painstaking manual labor.

Also I am attaching the “Station Style” HTML output for the citations from EndNote Desktop Application. This was generated with the forest-service-endnote-style CSL file that Sean Gordon created. It might need more work.

Same deal, sorted by Journal, and then sorted by Author.

We can discuss more in person, just wanted to write some notes down here to share.

I’m also attaching my spreadsheet. It is really a mess, I think the bottom line out of all this is there ought to be more features in RITS to permit PNW export all of the information that is entered in to RITS.

An alternative approach might be to get a program that scrapes the content from the TreeSearch XML documents – beyond my skill level at the moment but it’s an interesting problem to look at.

For now, the process I’ve come up with to arrive at the formatted bibliography below is probably more labor intensive than you want, but I think it provides info your readers would probably want to know, and it identifies publications that may not actually be “new” this quarter, just “new” to TreeSearch this quarter.

-Tanner

From: Tanner Jessel [mailto:]
Sent: Monday, April 17, 2017 9:55 AM
To: Jessel, Tanner – FS < >
Subject: PNW Quarterly Pubs

Agriculture and Human Values

Hummel, Susan Stevens. “E. N. Anderson: Caring for Place: Ecology, Ideology, and Emotion in Traditional Landscape Management.” Agriculture and Human Values 33, no. 2 (June 29, 2016): 495–96. doi:10.1007/s10460-016-9691-6.

Aquatic Conservation: Marine and Freshwater Ecosystems

Flitcroft, Rebecca L., Daniel L. Bottom, Karen L. Haberman, Ken F. Bierly, Kim K. Jones, Charles A. Simenstad, Ayesha Gray, et al. “Expect the Unexpected: Place-Based Protections Can Lead to Unforeseen Benefits.” Aquatic Conservation: Marine and Freshwater Ecosystems 26, no. S1 (June 2016): 39–59. doi:10.1002/aqc.2660.

Juffe-Bignoli, Diego, Ian Harrison, Stuart HM Butchart, Rebecca Flitcroft, Virgilio Hermoso, Harry Jonas, Anna Lukasiewicz, et al. “Achieving Aichi Biodiversity Target 11 to Improve the Performance of Protected Areas and Conserve Freshwater Biodiversity.” Aquatic Conservation: Marine and Freshwater Ecosystems 26, no. S1 (June 2016): 133–51. doi:10.1002/aqc.2638.

Juffe-Bignoli, Diego, Ian Harrison, Stuart HM Butchart, Rebecca Flitcroft, Virgilio Hermoso, Harry Jonas, Anna Lukasiewicz, et al. “Achieving Aichi Biodiversity Target 11 to Improve the Performance of Protected Areas and Conserve Freshwater Biodiversity.” Aquatic Conservation: Marine and Freshwater Ecosystems 26, no. S1 (June 2016): 133–51. doi:10.1002/aqc.2638.

Atmospheric Chemistry and Physics

Yokelson, R. J., I. R. Burling, J. B. Gilman, C. Warneke, C. E. Stockwell, J. de Gouw, S. K. Akagi, et al. “Coupling Field and Laboratory Measurements to Estimate the Emission Factors of Identified and Unidentified Trace Gases for Prescribed Fires.” Atmospheric Chemistry and Physics 13, no. 1 (January 7, 2013): 89–116. doi:10.5194/acp-13-89-2013.

Chakrabarty, Rajan K., Madhu Gyawali, Reddy L. N. Yatavelli, Apoorva Pandey, Adam C. Watts, Joseph Knue, Lung-Wen A. Chen, et al. “Brown Carbon Aerosols from Burning of Boreal Peatlands: Microphysical Properties, Emission Factors, and Implications for Direct Radiative Forcing.” Atmospheric Chemistry and Physics 16, no. 5 (March 9, 2016): 3033–40. doi:10.5194/acp-16-3033-2016.

BioScience

Arismendi, Ivan, and Brooke E. Penaluna. “Examining Diversity Inequities in Fisheries Science: A Call to Action.” BioScience 66, no. 7 (July 1, 2016): 584–91. doi:10.1093/biosci/biw041.

Canadian Journal of Forest Research

Eskelson, Bianca N.I., Vicente J. Monleon, and Jeremy S. Fried. “A 6 Year Longitudinal Study of Post-Fire Woody Carbon Dynamics in California’s Forests.” Canadian Journal of Forest Research 46, no. 5 (May 2016): 610–20. doi:10.1139/cjfr-2015-0375.

Caouette, J.P., E.A. Steel, P.E. Hennon, P.G. Cunningham, C.A. Pohl, and B.A. Schrader. “Influence of Elevation and Site Productivity on Conifer Distributions across Alaskan Temperate Rainforests.” Canadian Journal of Forest Research 46, no. 2 (February 2016): 249–61. doi:10.1139/cjfr-2015-0283.

Poudel, K.P., and H. Temesgen. “Methods for Estimating Aboveground Biomass and Its Components for Douglas-Fir and Lodgepole Pine Trees.” Canadian Journal of Forest Research 46, no. 1 (January 2016): 77–87. doi:10.1139/cjfr-2015-0256.

Canadian Journal of Remote Sensing

Vierling, Lee A., Yanyin Xu, Jan U H Eitel, and John S. Oldow. “Shrub Characterization Using Terrestrial Laser Scanning and Implications for Airborne LiDAR Assessment.” Canadian Journal of Remote Sensing 38, no. 6 (January 11, 2012): 709–22. doi:10.5589/m12-057.

Current Forestry Reports

Vaillant, Nicole M., Crystal A. Kolden, and Alistair M. S. Smith. “Assessing Landscape Vulnerability to Wildfire in the USA.” Current Forestry Reports 2, no. 3 (September 15, 2016): 201–13. doi:10.1007/s40725-016-0040-1.

Disasters

Zahran, Sammy, Samuel D. Brody, Walter Gillis Peacock, Arnold Vedlitz, Himanshu Grover, V Sturtevant, RF Brummel, et al. “Social Vulnerability and the Natural and Built Environment: A Model of Flood Casualties in Texas.” Disasters 32, no. 4 (December 2008): 537–60. doi:10.1111/j.1467-7717.2008.01054.x.

Diversity and Distributions

Zahran, Sammy, Samuel D. Brody, Walter Gillis Peacock, Arnold Vedlitz, Himanshu Grover, V Sturtevant, RF Brummel, et al. “Social Vulnerability and the Natural and Built Environment: A Model of Flood Casualties in Texas.” Disasters 32, no. 4 (December 2008): 537–60. doi:10.1111/j.1467-7717.2008.01054.x.

Ecological Applications

Kline, Jeffrey D., Mark E. Harmon, Thomas A. Spies, Anita T. Morzillo, Robert J. Pabst, Brenda C. McComb, Frank Schnekenburger, Keith A. Olsen, Blair Csuti, and Jody C. Vogeler. “Evaluating Carbon Storage, Timber Harvest, and Habitat Possibilities for a Western Cascades (USA) Forest Landscape.” Ecological Applications 26, no. 7 (October 2016): 2044–59. doi:10.1002/eap.1358.

Ecological Indicators

Kline, Jeffrey D., Mark E. Harmon, Thomas A. Spies, Anita T. Morzillo, Robert J. Pabst, Brenda C. McComb, Frank Schnekenburger, Keith A. Olsen, Blair Csuti, and Jody C. Vogeler. “Evaluating Carbon Storage, Timber Harvest, and Habitat Possibilities for a Western Cascades (USA) Forest Landscape.” Ecological Applications 26, no. 7 (October 2016): 2044–59. doi:10.1002/eap.1358.

Ecological Modelling

Bell, David M., and Daniel R. Schlaepfer. “On the Dangers of Model Complexity without Ecological Justification in Species Distribution Modeling.” Ecological Modelling 330 (2016): 50–59. doi:10.1016/j.ecolmodel.2016.03.012.

Ecology

Bansal, Sheel, Constance A. Harrington, and John Bradley St. Clair. “Tolerance to Multiple Climate Stressors: A Case Study of Douglas-Fir Drought and Cold Hardiness.” Ecology and Evolution 6, no. 7 (April 2016): 2074–83. doi:10.1002/ece3.2007.

Burton, Julia I., Deanna H. Olson, and Klaus J. Puettmann. “Effects of Riparian Buffer Width on Wood Loading in Headwater Streams after Repeated Forest Thinning.” Forest Ecology and Management 372 (2016): 247–57. doi:10.1016/j.foreco.2016.03.053.

Cowan, Ariel D., Jane E. Smith, and Stephen A. Fitzgerald. “Recovering Lost Ground: Effects of Soil Burn Intensity on Nutrients and Ectomycorrhiza Communities of Ponderosa Pine Seedlings.” Forest Ecology and Management 378 (2016): 160–72. doi:10.1016/j.foreco.2016.07.030.

Fischer, A Paige, Thomas A Spies, Toddi A Steelman, Cassandra Moseley, Bart R Johnson, John D Bailey, Alan A Ager, et al. “Wildfire Risk as a Socioecological Pathology.” Frontiers in Ecology and the Environment 14, no. 5 (June 2016): 276–84. doi:10.1002/fee.1283.

Flitcroft, Rebecca L., Jeffrey A. Falke, Gordon H. Reeves, Paul F. Hessburg, Kris M. McNyset, and Lee E. Benda. “Wildfire May Increase Habitat Quality for Spring Chinook Salmon in the Wenatchee River Subbasin, WA, USA.” Forest Ecology and Management 359 (2016): 126–40. doi:10.1016/j.foreco.2015.09.049.

Halpern, Charles B., Joseph A. Antos, Donald McKenzie, and Annette M. Olson. “Past Tree Influence and Prescribed Fire Mediate Biotic Interactions and Community Reassembly in a Grassland-Restoration Experiment.” Edited by Lara Souza. Journal of Applied Ecology 53, no. 1 (February 2016): 264–73. doi:10.1111/1365-2664.12570.

Hessburg, Paul F., Thomas A. Spies, David A. Perry, Carl N. Skinner, Alan H. Taylor, Peter M. Brown, Scott L. Stephens, et al. “Tamm Review: Management of Mixed-Severity Fire Regime Forests in Oregon, Washington, and Northern California.” Forest Ecology and Management 366 (2016): 221–50. doi:10.1016/j.foreco.2016.01.034.

Hessburg, Paul F., Thomas A. Spies, David A. Perry, Carl N. Skinner, Alan H. Taylor, Peter M. Brown, Scott L. Stephens, et al. “Tamm Review: Management of Mixed-Severity Fire Regime Forests in Oregon, Washington, and Northern California.” Forest Ecology and Management 366 (2016): 221–50. doi:10.1016/j.foreco.2016.01.034.

Hewitt, Rebecca E., Alec P. Bennett, Amy L. Breen, Teresa N. Hollingsworth, D. Lee Taylor, F. Stuart Chapin, and T. Scott Rupp. “Getting to the Root of the Matter: Landscape Implications of Plant-Fungal Interactions for Tree Migration in Alaska.” Landscape Ecology 31, no. 4 (May 14, 2016): 895–911. doi:10.1007/s10980-015-0306-1.

Kelsey, Rick G., Gladwin Joseph, Doug Westlind, and Walter G. Thies. “Ethanol and Acetone from Douglas-Fir Roots Stressed by Phellinus Sulphurascens Infection: Implications for Detecting Diseased Trees and for Beetle Host Selection.” Forest Ecology and Management 360 (2016): 261–72. doi:10.1016/j.foreco.2015.10.039.

Lorenz, Teresa J., Kerri T. Vierling, Jeffrey M. Kozma, and Janet E. Millard. “Foraging Plasticity by a Keystone Excavator, the White-Headed Woodpecker, in Managed Forests: Are There Consequences for Productivity?” Forest Ecology and Management 363 (2016): 110–19. doi:10.1016/j.foreco.2015.12.021.

Maffei, Helen M., Gregory M. Filip, Nancy E. Grulke, Brent W. Oblinger, Ellis Q. Margolis, and Kristen L. Chadwick. “Pruning High-Value Douglas-Fir Can Reduce Dwarf Mistletoe Severity and Increase Longevity in Central Oregon.” Forest Ecology and Management 379 (2016): 11–19. doi:10.1016/j.foreco.2016.07.014.

Reazin, C., S. Morris, J.E. Smith, A.D. Cowan, and A. Jumpponen. “Fires of Differing Intensities Rapidly Select Distinct Soil Fungal Communities in a Northwest US Ponderosa Pine Forest Ecosystem.” Forest Ecology and Management 377 (2016): 118–27. doi:10.1016/j.foreco.2016.07.002.

Slesak, Robert A., Timothy B. Harrington, David H. Peter, Daniel G. DeBruler, Stephen H. Schoenholtz, and Brian D. Strahm. “Effects of Intensive Management Practices on 10-Year Douglas-Fir Growth, Soil Nutrient Pools, and Vegetation Communities in the Pacific Northwest, USA.” Forest Ecology and Management 365 (2016): 22–33. doi:10.1016/j.foreco.2016.01.019.

Varner, J. Morgan, Mary A. Arthur, Stacy L. Clark, Daniel C. Dey, Justin L. Hart, and Callie Jo Schweitzer. “Fire in Eastern North American Oak Ecosystems: Filling the Gaps.” Fire Ecology 12, no. 2 (August 2016): 1–6. doi:10.4996/fireecology.1202001.

White, Alan S., SH Doerr, RPD Walsh, A Shanklin, and JL Jonas. “Presettlement Regeneration Patterns in a Southwestern Ponderosa Pine Stand.” Ecology 66, no. 2 (April 1985): 589–94. doi:10.2307/1940407.

Whittier, Thomas R., and Andrew N. Gray. “Tree Mortality Based Fire Severity Classification for Forest Inventories: A Pacific Northwest National Forests Example.” Forest Ecology and Management 359 (2016): 199–209. doi:10.1016/j.foreco.2015.10.015.

Wright, Clinton S., RJ Mitchell, JJ Hendricks, LR Boring, CW Berisford, J Aurell, A Holder, et al. “Models for Predicting Fuel Consumption in Sagebrush-Dominated Ecosystems.” Rangeland Ecology & Management 66, no. 3 (May 2013): 254–66. doi:10.2111/REM-D-12-00027.1.

Zald, Harold S.J., Thomas A. Spies, Rupert Seidl, Robert J. Pabst, Keith A. Olsen, and E. Ashley Steel. “Complex Mountain Terrain and Disturbance History Drive Variation in Forest Aboveground Live Carbon Density in the Western Oregon Cascades, USA.” Forest Ecology and Management 366 (2016): 193–207. doi:10.1016/j.foreco.2016.01.036.

Ecology and Evolution

Bansal, Sheel, Constance A. Harrington, and John Bradley St. Clair. “Tolerance to Multiple Climate Stressors: A Case Study of Douglas-Fir Drought and Cold Hardiness.” Ecology and Evolution 6, no. 7 (April 2016): 2074–83. doi:10.1002/ece3.2007.

Ecosphere

Atwood, Todd C., Bruce G. Marcot, David C. Douglas, Steven C. Amstrup, Karyn D. Rode, George M. Durner, and Jeffrey F. Bromaghin. “Forecasting the Relative Influence of Environmental and Anthropogenic Stressors on Polar Bears.” Ecosphere 7, no. 6 (June 2016): e01370. doi:10.1002/ecs2.1370.

Gray, Andrew N., Thomas R. Whittier, and Mark E. Harmon. “Carbon Stocks and Accumulation Rates in Pacific Northwest Forests: Role of Stand Age, Plant Community, and Productivity.” Edited by D. P. Peters. Ecosphere 7, no. 1 (January 2016): e01224. doi:10.1002/ecs2.1224.

Ecosystem Services

Schroder, Svetlana A. (Kushch), Sándor F. Tóth, Robert L. Deal, and Gregory J. Ettl. “Multi-Objective Optimization to Evaluate Tradeoffs among Forest Ecosystem Services Following Fire Hazard Reduction in the Deschutes National Forest, USA.” Ecosystem Services 22 (2016): 328–47. doi:10.1016/j.ecoser.2016.08.006.

Environmental Research Letters

Abbott, Benjamin W, Jeremy B Jones, Edward A G Schuur, F Stuart Chapin III, William B Bowden, M Syndonia Bret-Harte, Howard E Epstein, et al. “Biomass Offsets Little or None of Permafrost Carbon Release from Soils, Streams, and Wildfire: An Expert Assessment.” Environmental Research Letters 11, no. 3 (March 1, 2016): 34014. doi:10.1088/1748-9326/11/3/034014.

Fire Ecology

Varner, J. Morgan, Mary A. Arthur, Stacy L. Clark, Daniel C. Dey, Justin L. Hart, and Callie Jo Schweitzer. “Fire in Eastern North American Oak Ecosystems: Filling the Gaps.” Fire Ecology 12, no. 2 (August 2016): 1–6. doi:10.4996/fireecology.1202001.

Fisheries

Penaluna, Brooke E., Alicia Abadía-Cardoso, Jason B. Dunham, Francisco J. García-Dé León, Robert E. Gresswell, Arturo Ruiz Luna, Eric B. Taylor, et al. “Conservation of Native Pacific Trout Diversity in Western North America.” Fisheries 41, no. 6 (June 2, 2016): 286–300. doi:10.1080/03632415.2016.1175888.

Hance, Dalton J., Lisa M. Ganio, Kelly M. Burnett, and Joseph L. Ebersole. “Basin-Scale Variation in the Spatial Pattern of Fall Movement of Juvenile Coho Salmon in the West Fork Smith River, Oregon.” Transactions of the American Fisheries Society 145, no. 5 (September 2, 2016): 1018–34. doi:10.1080/00028487.2016.1194892.

Forest Ecology and Management

Cowan, Ariel D., Jane E. Smith, and Stephen A. Fitzgerald. “Recovering Lost Ground: Effects of Soil Burn Intensity on Nutrients and Ectomycorrhiza Communities of Ponderosa Pine Seedlings.” Forest Ecology and Management 378 (2016): 160–72. doi:10.1016/j.foreco.2016.07.030.

Maffei, Helen M., Gregory M. Filip, Nancy E. Grulke, Brent W. Oblinger, Ellis Q. Margolis, and Kristen L. Chadwick. “Pruning High-Value Douglas-Fir Can Reduce Dwarf Mistletoe Severity and Increase Longevity in Central Oregon.” Forest Ecology and Management 379 (2016): 11–19. doi:10.1016/j.foreco.2016.07.014.

Reazin, C., S. Morris, J.E. Smith, A.D. Cowan, and A. Jumpponen. “Fires of Differing Intensities Rapidly Select Distinct Soil Fungal Communities in a Northwest US Ponderosa Pine Forest Ecosystem.” Forest Ecology and Management 377 (2016): 118–27. doi:10.1016/j.foreco.2016.07.002.

Burton, Julia I., Deanna H. Olson, and Klaus J. Puettmann. “Effects of Riparian Buffer Width on Wood Loading in Headwater Streams after Repeated Forest Thinning.” Forest Ecology and Management 372 (2016): 247–57. doi:10.1016/j.foreco.2016.03.053.

Zald, Harold S.J., Thomas A. Spies, Rupert Seidl, Robert J. Pabst, Keith A. Olsen, and E. Ashley Steel. “Complex Mountain Terrain and Disturbance History Drive Variation in Forest Aboveground Live Carbon Density in the Western Oregon Cascades, USA.” Forest Ecology and Management 366 (2016): 193–207. doi:10.1016/j.foreco.2016.01.036.

Hessburg, Paul F., Thomas A. Spies, David A. Perry, Carl N. Skinner, Alan H. Taylor, Peter M. Brown, Scott L. Stephens, et al. “Tamm Review: Management of Mixed-Severity Fire Regime Forests in Oregon, Washington, and Northern California.” Forest Ecology and Management 366 (2016): 221–50. doi:10.1016/j.foreco.2016.01.034.

Hessburg, Paul F., Thomas A. Spies, David A. Perry, Carl N. Skinner, Alan H. Taylor, Peter M. Brown, Scott L. Stephens, et al. “Tamm Review: Management of Mixed-Severity Fire Regime Forests in Oregon, Washington, and Northern California.” Forest Ecology and Management 366 (2016): 221–50. doi:10.1016/j.foreco.2016.01.034.

Slesak, Robert A., Timothy B. Harrington, David H. Peter, Daniel G. DeBruler, Stephen H. Schoenholtz, and Brian D. Strahm. “Effects of Intensive Management Practices on 10-Year Douglas-Fir Growth, Soil Nutrient Pools, and Vegetation Communities in the Pacific Northwest, USA.” Forest Ecology and Management 365 (2016): 22–33. doi:10.1016/j.foreco.2016.01.019.

Lorenz, Teresa J., Kerri T. Vierling, Jeffrey M. Kozma, and Janet E. Millard. “Foraging Plasticity by a Keystone Excavator, the White-Headed Woodpecker, in Managed Forests: Are There Consequences for Productivity?” Forest Ecology and Management 363 (2016): 110–19. doi:10.1016/j.foreco.2015.12.021.

Kelsey, Rick G., Gladwin Joseph, Doug Westlind, and Walter G. Thies. “Ethanol and Acetone from Douglas-Fir Roots Stressed by Phellinus Sulphurascens Infection: Implications for Detecting Diseased Trees and for Beetle Host Selection.” Forest Ecology and Management 360 (2016): 261–72. doi:10.1016/j.foreco.2015.10.039.

Whittier, Thomas R., and Andrew N. Gray. “Tree Mortality Based Fire Severity Classification for Forest Inventories: A Pacific Northwest National Forests Example.” Forest Ecology and Management 359 (2016): 199–209. doi:10.1016/j.foreco.2015.10.015.

Flitcroft, Rebecca L., Jeffrey A. Falke, Gordon H. Reeves, Paul F. Hessburg, Kris M. McNyset, and Lee E. Benda. “Wildfire May Increase Habitat Quality for Spring Chinook Salmon in the Wenatchee River Subbasin, WA, USA.” Forest Ecology and Management 359 (2016): 126–40. doi:10.1016/j.foreco.2015.09.049.

Forest Policy and Economics

Latta, Gregory S., Darius M. Adams, Kathleen P. Bell, and Jeffrey D. Kline. “Evaluating Land-Use and Private Forest Management Responses to a Potential Forest Carbon Offset Sales Program in Western Oregon (USA).” Forest Policy and Economics 65 (2016): 1–8. doi:10.1016/j.forpol.2016.01.004.

Donovan, Geoffrey H., Lee K. Cerveny, and Demetrios Gatziolis. “If You Build It, Will They Come?” Forest Policy and Economics 62 (2016): 135–40. doi:10.1016/j.forpol.2015.11.002.

Forests

Poudel, Krishna, and Hailemariam Temesgen. “Developing Biomass Equations for Western Hemlock and Red Alder Trees in Western Oregon Forests.” Forests 7, no. 4 (April 21, 2016): 88. doi:10.3390/f7040088.

Frontiers in Ecology and the Environment

Fischer, A Paige, Thomas A Spies, Toddi A Steelman, Cassandra Moseley, Bart R Johnson, John D Bailey, Alan A Ager, et al. “Wildfire Risk as a Socioecological Pathology.” Frontiers in Ecology and the Environment 14, no. 5 (June 2016): 276–84. doi:10.1002/fee.1283.

Frontiers in Plant Science

Syring, John V., Jacob A. Tennessen, Tara N. Jennings, Jill Wegrzyn, Camille Scelfo-Dalbey, and Richard Cronn. “Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome.” Frontiers in Plant Science 7 (April 21, 2016): 484. doi:10.3389/fpls.2016.00484.

Global Change Biology

Littell, Jeremy S., David L. Peterson, Karin L. Riley, Yongquiang Liu, and Charles H. Luce. “A Review of the Relationships between Drought and Forest Fire in the United States.” Global Change Biology 22, no. 7 (July 2016): 2353–69. doi:10.1111/gcb.13275.

Black, Bryan A., Daniel Griffin, Peter van der Sleen, Alan D. Wanamaker, James H. Speer, David C. Frank, David W. Stahle, et al. “The Value of Crossdating to Retain High-Frequency Variability, Climate Signals, and Extreme Events in Environmental Proxies.” Global Change Biology 22, no. 7 (July 2016): 2582–95. doi:10.1111/gcb.13256.

Voelker, Steven L., J. Renée Brooks, Frederick C. Meinzer, Rebecca Anderson, Martin K.-F. Bader, Giovanna Battipaglia, Katie M. Becklin, et al. “A Dynamic Leaf Gas-Exchange Strategy Is Conserved in Woody Plants under Changing Ambient CO 2 : Evidence from Carbon Isotope Discrimination in Paleo and CO 2 Enrichment Studies.” Global Change Biology 22, no. 2 (February 2016): 889–902. doi:10.1111/gcb.13102.

Hydrology and Earth System Sciences

Fu, Congsheng, Guiling Wang, Michael L. Goulden, Russell L. Scott, Kenneth Bible, and Zoe G. Cardon. “Combined Measurement and Modeling of the Hydrological Impact of Hydraulic Redistribution Using CLM4.5 at Eight AmeriFlux Sites.” Hydrology and Earth System Sciences 20, no. 5 (May 17, 2016): 2001–18. doi:10.5194/hess-20-2001-2016.

Inhalation Toxicology

Adetona, Olorunfemi, Timothy E. Reinhardt, Joe Domitrovich, George Broyles, Anna M. Adetona, Michael T. Kleinman, Roger D. Ottmar, and Luke P. Naeher. “Review of the Health Effects of Wildland Fire Smoke on Wildland Firefighters and the Public.” Inhalation Toxicology 28, no. 3 (February 23, 2016): 95–139. doi:10.3109/08958378.2016.1145771.

International Journal of Wildland Fire

Prestemon, Jeffrey P., Uma Shankar, Aijun Xiu, K. Talgo, D. Yang, Ernest Dixon, Donald McKenzie, and Karen L. Abt. “Projecting Wildfire Area Burned in the South-Eastern United States, 2011–60.” International Journal of Wildland Fire 25, no. 7 (2016): 715. doi:10.1071/WF15124.

Journal of Applied Ecology

Halpern, Charles B., Joseph A. Antos, Donald McKenzie, and Annette M. Olson. “Past Tree Influence and Prescribed Fire Mediate Biotic Interactions and Community Reassembly in a Grassland-Restoration Experiment.” Edited by Lara Souza. Journal of Applied Ecology 53, no. 1 (February 2016): 264–73. doi:10.1111/1365-2664.12570.

Journal of Environmental Management

Buotte, Polly C., David L. Peterson, Kevin S. McKelvey, and Jeffrey A. Hicke. “Capturing Subregional Variability in Regional-Scale Climate Change Vulnerability Assessments of Natural Resources.” Journal of Environmental Management 169 (2016): 313–18. doi:10.1016/j.jenvman.2015.12.017.

Journal of Environmental Planning and Management

Buotte, Polly C., David L. Peterson, Kevin S. McKelvey, and Jeffrey A. Hicke. “Capturing Subregional Variability in Regional-Scale Climate Change Vulnerability Assessments of Natural Resources.” Journal of Environmental Management 169 (2016): 313–18. doi:10.1016/j.jenvman.2015.12.017.

Journal of Environmental Studies and Sciences

Batavia, Chelsea, and Michael Paul Nelson. “Heroes or Thieves? The Ethical Grounds for Lingering Concerns about New Conservation.” Journal of Environmental Studies and Sciences, May 6, 2016, 1–9. doi:10.1007/s13412-016-0399-0.

Journal of Field Ornithology

Wilk, Randall J., Martin G. Raphael, and Thomas D. Bloxton. “Nesting Habitat Characteristics of Marbled Murrelets Occurring in near-Shore Waters of the Olympic Peninsula, Washington.” Journal of Field Ornithology 87, no. 2 (June 2016): 162–75. doi:10.1111/jofo.12150.

Journal of Forestry

Zald, Harold S.J., Thomas A. Spies, Mark E. Harmon, and Mark J. Twery. “Forest Carbon Calculators: A Review for Managers, Policymakers, and Educators.” Journal of Forestry 114, no. 2 (March 16, 2016): 134–43. doi:10.5849/jof.15-019.

Reich, Robin M., John E. Lundquist, and Kristina Hughes. “Host-Environment Mismatches Associated with Subalpine Fir Decline in Colorado.” Journal of Forestry Research 27, no. 5 (October 19, 2016): 1177–89. doi:10.1007/s11676-016-0234-1.

Journal of Theoretical Biology

Hamelin, Frédéric M., Linda J.S. Allen, Holly R. Prendeville, M. Reza Hajimorad, and Michael J. Jeger. “The Evolution of Plant Virus Transmission Pathways.” Journal of Theoretical Biology 396 (2016): 75–89. doi:10.1016/j.jtbi.2016.02.017.

Landscape and Urban Planning

Ager, Alan A., Michelle A. Day, Karen C. Short, and Cody R. Evers. “Assessing the Impacts of Federal Forest Planning on Wildfire Risk Mitigation in the Pacific Northwest, USA.” Landscape and Urban Planning 147 (2016): 1–17. doi:10.1016/j.landurbplan.2015.11.007.

Lee, Yohan, Claire A. Montgomery, and Jeffrey D. Kline. “The Influence of Age-Specific Migration on Housing Growth in the Rural Midwest (USA).” Landscape and Urban Planning 148 (2016): 68–79. doi:10.1016/j.landurbplan.2015.12.005.

Fischer, A. Paige, Ken Vance-Borland, Lorien Jasny, Kerry E. Grimm, and Susan Charnley. “A Network Approach to Assessing Social Capacity for Landscape Planning: The Case of Fire-Prone Forests in Oregon, USA.” Landscape and Urban Planning 147 (2016): 18–27. doi:10.1016/j.landurbplan.2015.10.006.

Landscape Ecology

Hewitt, Rebecca E., Alec P. Bennett, Amy L. Breen, Teresa N. Hollingsworth, D. Lee Taylor, F. Stuart Chapin, and T. Scott Rupp. “Getting to the Root of the Matter: Landscape Implications of Plant-Fungal Interactions for Tree Migration in Alaska.” Landscape Ecology 31, no. 4 (May 14, 2016): 895–911. doi:10.1007/s10980-015-0306-1.

Measurement

Liénard, Jean, Andre Vogs, Demetrios Gatziolis, and Nikolay Strigul. “Embedded, Real-Time UAV Control for Improved, Image-Based 3D Scene Reconstruction.” Measurement 81 (2016): 264–69. doi:10.1016/j.measurement.2015.12.014.

Mycologia

Hobbie, Erik A., Samuel F. Rice, Nancy S. Weber, and Jane E. Smith. “Isotopic Evidence Indicates Saprotrophy in Post-Fire Morchella in Oregon and Alaska.” Mycologia 108, no. 4 (July 20, 2016): 638–45. doi:10.3852/15-281.

Mycorrhiza

Hobbie, Erik A., Samuel F. Rice, Nancy S. Weber, and Jane E. Smith. “Isotopic Evidence Indicates Saprotrophy in Post-Fire Morchella in Oregon and Alaska.” Mycologia 108, no. 4 (July 20, 2016): 638–45. doi:10.3852/15-281.

Natural Areas Journal

DeBano, Sandra J., Samantha M. Roof, Mary M. Rowland, and Lauren A. Smith. “Diet Overlap of Mammalian Herbivores and Native Bees: Implications for Managing Co-Occurring Grazers and Pollinators.” Natural Areas Journal 36, no. 4 (October 2016): 458–77. doi:10.3375/043.036.0412.

Northwestern Naturalist

Moriarty, Katie M, John D Bailey, Sharon E Smythe, and Jake Verschuyl. “Distribution of Pacific Marten in Coastal Oregon.” Northwestern Naturalist 97, no. 2 (January 2016): 71–81. doi:10.1898/NWN16-01.1.

Moriarty, Katie M, John D Bailey, Sharon E Smythe, and Jake Verschuyl. “Distribution of Pacific Marten in Coastal Oregon.” Northwestern Naturalist 97, no. 2 (January 2016): 71–81. doi:10.1898/NWN16-01.1.

Oecologia

Long, Ryan A., R. T. Bowyer, Warren P. Porter, Paul Mathewson, Kevin L. Monteith, Scott L. Findholt, Brian L. Dick, and John G. Kie. “Linking Habitat Selection to Fitness-Related Traits in Herbivores: The Role of the Energy Landscape.” Oecologia 181, no. 3 (July 22, 2016): 709–20. doi:10.1007/s00442-016-3604-7.

Bell, David M., and James S. Clark. “Seed Predation and Climate Impacts on Reproductive Variation in Temperate Forests of the Southeastern USA.” Oecologia 180, no. 4 (April 8, 2016): 1223–34. doi:10.1007/s00442-015-3537-6.

Plant and Soil

Slesak, Robert A., Timothy B. Harrington, and Anthony W. D’Amato. “Invasive Scotch Broom Alters Soil Chemical Properties in Douglas-Fir Forests of the Pacific Northwest, USA.” Plant and Soil 398, no. 1–2 (January 14, 2016): 281–89. doi:10.1007/s11104-015-2662-7.

PLOS ONE

Lorenz, Teresa J., Martin G. Raphael, Thomas D. Bloxton, RJ van Aarde, T Duchesne, JS Mao, and Y Watanuki. “Marine Habitat Selection by Marbled Murrelets (Brachyramphus Marmoratus) during the Breeding Season.” Edited by Christian Andrew Hagen. PLOS ONE 11, no. 9 (September 28, 2016): e0162670. doi:10.1371/journal.pone.0162670.

Xie, Gisselle Yang, Deanna H. Olson, Andrew R. Blaustein, PTJ Johnson, SH Paull, and S Young. “Projecting the Global Distribution of the Emerging Amphibian Fungal Pathogen, Batrachochytrium Dendrobatidis, Based on IPCC Climate Futures.” Edited by Stefan Lötters. PLOS ONE 11, no. 8 (August 11, 2016): e0160746. doi:10.1371/journal.pone.0160746.

Schroeder, Hilke, Richard Cronn, Yulai Yanbaev, Tara Jennings, Malte Mader, Bernd Degen, and Birgit Kersten. “Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. Sect. Quercus).” Edited by Dusan Gomory. PLOS ONE 11, no. 6 (June 28, 2016): e0158221. doi:10.1371/journal.pone.0158221.

Edwards, Patrick M., S Johnson, L Sobota, J Banks, and B Gray. “The Value of Long-Term Stream Invertebrate Data Collected by Citizen Scientists.” Edited by Stefano Goffredo. PLOS ONE 11, no. 4 (April 27, 2016): e0153713. doi:10.1371/journal.pone.0153713.

Averett, Joshua P., Bruce McCune, Catherine G. Parks, Bridgett J. Naylor, Tim DelCurto, Ricardo Mata-González, and BD Maxwell. “Non-Native Plant Invasion along Elevation and Canopy Closure Gradients in a Middle Rocky Mountain Ecosystem.” Edited by RunGuo Zang. PLOS ONE 11, no. 1 (January 29, 2016): e0147826. doi:10.1371/journal.pone.0147826.

Gompper, Matthew E., Damon B. Lesmeister, Justina C. Ray, Jay R. Malcolm, Roland Kays, and GM Thompson. “Differential Habitat Use or Intraguild Interactions: What Structures a Carnivore Community?” Edited by Aaron W. Reed. PLOS ONE 11, no. 1 (January 5, 2016): e0146055. doi:10.1371/journal.pone.0146055.

Fortin, Jennifer K., Karyn D. Rode, Grant V. Hilderbrand, James Wilder, Sean Farley, Carole Jorgensen, and Bruce G. Marcot. “Impacts of Human Recreation on Brown Bears (Ursus Arctos): A Review and New Management Tool.” Edited by Daniel E Crocker. PLOS ONE 11, no. 1 (January 5, 2016): e0141983. doi:10.1371/journal.pone.0141983.

Proceedings of the National Academy of Sciences of the United States of America

Restaino, Christina M, David L Peterson, and Jeremy Littell. “Increased Water Deficit Decreases Douglas Fir Growth throughout Western US Forests.” Proceedings of the National Academy of Sciences of the United States of America 113, no. 34 (August 23, 2016): 9557–62. doi:10.1073/pnas.1602384113.

Simkin, Samuel M, Edith B Allen, William D Bowman, Christopher M Clark, Jayne Belnap, Matthew L Brooks, Brian S Cade, et al. “Conditional Vulnerability of Plant Diversity to Atmospheric Nitrogen Deposition across the United States.” Proceedings of the National Academy of Sciences of the United States of America 113, no. 15 (April 12, 2016): 4086–91. doi:10.1073/pnas.1515241113.

Rangeland Ecology & Management

Wright, Clinton S., RJ Mitchell, JJ Hendricks, LR Boring, CW Berisford, J Aurell, A Holder, et al. “Models for Predicting Fuel Consumption in Sagebrush-Dominated Ecosystems.” Rangeland Ecology & Management 66, no. 3 (May 2013): 254–66. doi:10.2111/REM-D-12-00027.1.

Remote Sensing of Environment

Gregoire, Timothy G., Erik Næsset, Ronald E. McRoberts, Göran Ståhl, Hans-Erik Andersen, Terje Gobakken, Liviu Ene, and Ross Nelson. “Statistical Rigor in LiDAR-Assisted Estimation of Aboveground Forest Biomass.” Remote Sensing of Environment 173 (2016): 98–108. doi:10.1016/j.rse.2015.11.012.

Scandinavian Journal of Forest Research

Gregoire, Timothy G., Erik Næsset, Ronald E. McRoberts, Göran Ståhl, Hans-Erik Andersen, Terje Gobakken, Liviu Ene, and Ross Nelson. “Statistical Rigor in LiDAR-Assisted Estimation of Aboveground Forest Biomass.” Remote Sensing of Environment 173 (2016): 98–108. doi:10.1016/j.rse.2015.11.012.

Science of The Total Environment

Syring, John V., Jacob A. Tennessen, Tara N. Jennings, Jill Wegrzyn, Camille Scelfo-Dalbey, and Richard Cronn. “Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome.” Frontiers in Plant Science 7 (April 21, 2016): 484. doi:10.3389/fpls.2016.00484.

Chapin, F. S., Teresa N. Hollingsworth, F. Stuart Chapin III, D. Lee Taylor, JR Key, AH Lloyd, AD McGuire, TS Rupp, AH Lynch, and JP Schimel. “Role of Land-Surface Changes in Arctic Summer Warming.” Science 310, no. 5748 (October 28, 2005): 657–60. doi:10.1126/science.1117368.

Hicks, Christina C., Arielle Levine, Arun Agrawal, Xavier Basurto, Sara J. Breslow, Courtney Carothers, Susan Charnley, et al. “Engage Key Social Concepts for Sustainability.” Science 352, no. 6281 (2016). http://science.sciencemag.org/content/352/6281/38.

Frey, Sarah J. K., Adam S. Hadley, Sherri L. Johnson, Mark Schulze, Julia A. Jones, and Matthew G. Betts. “Spatial Models Reveal the Microclimatic Buffering Capacity of Old-Growth Forests.” Science Advances 2, no. 4 (2016). http://advances.sciencemag.org/content/2/4/e1501392.

Wu, Zhiwei, Hong S. He, Zhihua Liu, Yu Liang, M Solino, P Duce, D Spano, and Z Zhu. “Comparing Fuel Reduction Treatments for Reducing Wildfire Size and Intensity in a Boreal Forest Landscape of Northeastern China.” Science of The Total Environment 454–455, no. Suppl (June 2013): 30–39. doi:10.1016/j.scitotenv.2013.02.058.

Donovan, Geoffrey H., Sarah E. Jovan, Demetrios Gatziolis, Igor Burstyn, Yvonne L. Michael, Michael C. Amacher, and Vicente J. Monleon. “Using an Epiphytic Moss to Identify Previously Unknown Sources of Atmospheric Cadmium Pollution.” Science of The Total Environment 559 (2016): 84–93. doi:10.1016/j.scitotenv.2016.03.182.

Science Advances

Frey, Sarah J. K., Adam S. Hadley, Sherri L. Johnson, Mark Schulze, Julia A. Jones, and Matthew G. Betts. “Spatial Models Reveal the Microclimatic Buffering Capacity of Old-Growth Forests.” Science Advances 2, no. 4 (2016). http://advances.sciencemag.org/content/2/4/e1501392.

Science of The Total Environment

Wu, Zhiwei, Hong S. He, Zhihua Liu, Yu Liang, M Solino, P Duce, D Spano, and Z Zhu. “Comparing Fuel Reduction Treatments for Reducing Wildfire Size and Intensity in a Boreal Forest Landscape of Northeastern China.” Science of The Total Environment 454–455, no. Suppl (June 2013): 30–39. doi:10.1016/j.scitotenv.2013.02.058.

Donovan, Geoffrey H., Sarah E. Jovan, Demetrios Gatziolis, Igor Burstyn, Yvonne L. Michael, Michael C. Amacher, and Vicente J. Monleon. “Using an Epiphytic Moss to Identify Previously Unknown Sources of Atmospheric Cadmium Pollution.” Science of The Total Environment 559 (2016): 84–93. doi:10.1016/j.scitotenv.2016.03.182.

The Journal of Real Estate Finance and Economics

Wu, JunJie, Wenchao Xu, and Ralph J. Alig. “How Do the Location, Size and Budget of Open Space Conservation Affect Land Values?” The Journal of Real Estate Finance and Economics 52, no. 1 (January 21, 2016): 73–97. doi:10.1007/s11146-015-9506-3.

The Journal of Wildlife Management

Moriarty, Katie M., Clinton W. Epps, and William J. Zielinski. “Forest Thinning Changes Movement Patterns and Habitat Use by Pacific Marten.” The Journal of Wildlife Management 80, no. 4 (May 2016): 621–33. doi:10.1002/jwmg.1060.

Transactions of the American Fisheries Society

Moriarty, Katie M., Clinton W. Epps, and William J. Zielinski. “Forest Thinning Changes Movement Patterns and Habitat Use by Pacific Marten.” The Journal of Wildlife Management 80, no. 4 (May 2016): 621–33. doi:10.1002/jwmg.1060.

Urban Forestry & Urban Greening

Strunk, Jacob L., John R. Mills, Paul Ries, Hailemariam Temesgen, and Lacey Jeroue. “An Urban Forest-Inventory-and-Analysis Investigation in Oregon and Washington.” Urban Forestry & Urban Greening 18 (2016): 100–109. doi:10.1016/j.ufug.2016.04.006.

Mills, John R., Patrick Cunningham, and Geoffrey H. Donovan. “Urban Forests and Social Inequality in the Pacific Northwest.” Urban Forestry & Urban Greening 16 (2016): 188–96. doi:10.1016/j.ufug.2016.02.011.

Richardson, Jeffrey J, and L. Monika Moskal. “Urban Food Crop Production Capacity and Competition with the Urban Forest.” Urban Forestry & Urban Greening 15 (2016): 58–64. doi:10.1016/j.ufug.2015.10.006.

This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

FYyy-qq-pnw-pub-update_tasks.xlsx

This week “Inside the Forest Service”

Curious if this is visible to the public…

I used to read the old People Places and Things, or at least skim through it.

I will bet you few will read these articles in this “agile, web-based product.”

Would be interesting to see if they are tracking item use.

From: FS-Office of the Chief
Sent: Friday, April 21, 2017 12:09 PM
To: FS-All FS < >
Subject: This week "Inside the Forest Service"

Welcome to this week’s “Inside the Forest Service.” We hope you’re enjoying this agile, web-based product. Some of the articles to check out this week include:

· The Forest Service is helping forest wildlife in Vietnam

· Tongass National Forest is teaching kids how to become Junior Rangers with its exciting new publication

· Our employees are sharing their passions for natural resources with the next generation at high school job fair

We are uploading new content about what is going on around the Forest Service every day, so don’t forget to check back often.

On the Move

There were no acceptances this week.

This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

CAP SharePoint site

Matt,

I’m dying here for want of a robust color palette for sub headings – look how awful this thing I just made is:

https://ems-team.usda.gov/sites/fs-rd-pnwcap/QuarterlyPubUpdate/Home.aspx

Besides Heading 1” (SHOUTY) and Heading 2 (LESS SHOUTY), all I’ve got to work with are progressively lighter shades of gray that aren’t all that different from “Paragraph.” My “Alternate” headings aren’t much better; “Heading 4” and “Paragraph” look practically the same.

Can you please put some color in our world?

-Tanner

P.S. I don’t really have skin in the game since I’m leaving soon… but seriously, the option with the more diverse color pallette will probably make things like my tedious writing less painful to read through. Just a user experience trick from one communicator to another.

From: Burks, Matthew C -FS
Sent: Thursday, April 20, 2017 9:57 AM
To: FS-pdl pnw cap < >
Subject: CAP SharePoint site

Hi CAP,

Just wanted to let you know that I am going to begin working on our CAP SharePoint site. Nothing will be deleted, just rearranged and reorganized for browsing ease. Some of the links may change throughout this process. And some new apps may be added.

I’d like our CAP site to be a good example that I can use when working with other programs. If you have any trouble locating a document or page throughout this process just shoot me an email or find me on skype and I’ll help you find it.

Publishing; not to worry I won’t be touching anything on your sites at this point. Frank and I will get together before any changes are made there.

Thanks,

Matt

This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

Archiving FS Software?

https://data.fs.usda.gov/research/services/westernstubservices/productsservicesentry?product_id=&treesearch_id=52214

nev3mU_4Aspe

An important note: the treesearch ID is in the "View article…" XML link that comes from Top 20 Most Recent PNW Pubs

From Subject Received Size Categories

Top 20 PNW Pubs Ozone exposure and nitrogen deposition lowers root biomass of ponderosa pine in the San Bernardino Mountains California 3/17/2017 7 KB

Top 20 PNW Pubs Area burned in alpine treeline ecotones reflects regionwide trends 3/17/2017 6 KB

Top 20 PNW Pubs Response of giant sequoia canopy foliage to elevated concentrations of atmospheric ozone 3/17/2017 8 KB

Top 20 PNW Pubs Transient nature of CO2 fertilization in arctic tundra 3/16/2017 7 KB

So, you would be able to skip a lot of the below steps?

Install Firefox

Add a new function: "Open Multiple URLS"

https://addons.mozilla.org/en-US/firefox/addon/open-multiple-urls/?src=api

Opens a list of multiple URLs from a supplied list of URLS, in plain text format.

Put this in one column:

https://www.treesearch.fs.fed.us/search.php?in_words_phrases=

Put the names of the publications with + instead of "space" in the next column.

Copy and paste both columns here:

http://textmechanic.com/text-tools/basic-text-tools/find-and-replace-text/

NOte: Is there a python command module that can do this?

COmbine them by "finding" the tab and "replacing" with nothing.

It is better to do this in a text editor Like NOtepad++ or TextWrangler but this is the best alternative I could find.

actions for "find and replace" in a text editor to prepare the data for the FirefOx link add-on:

Step 1 – prepare URL string by creating TreeSearch compatible search query: Find "space" and replace with with "+"

Step 2 – prepare URL string by combining TreeSearch text query with compatible search string: Find "tabs" (five spaces) and replace with "nothing" (i.e., delete all tabs so you have one continuous string)

The desired outcome is a whole list of URL search strings that look like this:

https://www.treesearch.fs.fed.us/search.php?in_words_phrases=Phenology+of+Pacific+Northwest+tree+species

Copy and paste all that into a new Notepad (plain text document)

Save it.

Copy and paste all that plain text into your Firefox add-on.

You should see a result that matches your search string. There may be a few, rely on your human brain to choose the right one.

COpy and past the URL for teh correct result. For the example above, that is the following URL:

https://www.treesearch.fs.fed.us/pubs/53128

Scroll all the way back (left arrow on your browser tabs in Firefox)

Start copying and pasting URLs.

Ctrl+W as you go along will close each tab as you proceed through.

You might encounter some hitches. Example:

https://www.treesearch.fs.fed.us/search.php?in_words_phrases=Annotated+bibliography+of+the+red+tree+vole+(Arborimus+longicaudus),+Sonoma+tree+vole+(A.+pomo),+and+white-footed+vole+(A.+albipes).

Possibly failed due to non-coded parenthetical.

Executing the search again, with the problem character removed (paranthetical in this case, yeilds success)

Example:

https://www.treesearch.fs.fed.us/search.php?in_words_phrases=Annotated+bibliography+of+the+red+tree+vole

Note "NA" if your automated search (and attempt at fixing problem searches, as above) did not retrieve results.

If there is a problem with a record, highlight it in red.

Example – a RITS record with typographical errors:

Dam Rmoval Iformation Prtal (DRIP)—A map-based resource linking scientific studies and associated geospatial information about dam removals: U.S

Dam Removal Information Portal (DRIP)—A map-based resource linking scientific studies and associated geospatial information about dam removals: U.S

Sort by TreeSearch ID (Column D)

TreeSearch_ID

Copy out all the URLS which contain the TreeSearch ID. In this example, it was 148 out of total 178. Two were "not found" and one was a "reject."

https://www.treesearch.fs.fed.us/pubs/49896

https://www.treesearch.fs.fed.us/pubs/49900

https://www.treesearch.fs.fed.us/pubs/50056

https://www.treesearch.fs.fed.us/pubs/50057

https://www.treesearch.fs.fed.us/pubs/50067

https://www.treesearch.fs.fed.us/pubs/50115

https://www.treesearch.fs.fed.us/pubs/50198

https://www.treesearch.fs.fed.us/pubs/50199

https://www.treesearch.fs.fed.us/pubs/50200

https://www.treesearch.fs.fed.us/pubs/50263

https://www.treesearch.fs.fed.us/pubs/50332

https://www.treesearch.fs.fed.us/pubs/50397

https://www.treesearch.fs.fed.us/pubs/50400

https://www.treesearch.fs.fed.us/pubs/50402

https://www.treesearch.fs.fed.us/pubs/50464

https://www.treesearch.fs.fed.us/pubs/50468

https://www.treesearch.fs.fed.us/pubs/50503

https://www.treesearch.fs.fed.us/pubs/50530

https://www.treesearch.fs.fed.us/pubs/50567

https://www.treesearch.fs.fed.us/pubs/50656

https://www.treesearch.fs.fed.us/pubs/50697

https://www.treesearch.fs.fed.us/pubs/50788

https://www.treesearch.fs.fed.us/pubs/50789

https://www.treesearch.fs.fed.us/pubs/50790

https://www.treesearch.fs.fed.us/pubs/50791

https://www.treesearch.fs.fed.us/pubs/50882

https://www.treesearch.fs.fed.us/pubs/50909

https://www.treesearch.fs.fed.us/pubs/50910

https://www.treesearch.fs.fed.us/pubs/50914

https://www.treesearch.fs.fed.us/pubs/50915

https://www.treesearch.fs.fed.us/pubs/50916

https://www.treesearch.fs.fed.us/pubs/50917

https://www.treesearch.fs.fed.us/pubs/50918

https://www.treesearch.fs.fed.us/pubs/50919

https://www.treesearch.fs.fed.us/pubs/50935

https://www.treesearch.fs.fed.us/pubs/50952

https://www.treesearch.fs.fed.us/pubs/50970

https://www.treesearch.fs.fed.us/pubs/50985

https://www.treesearch.fs.fed.us/pubs/51057

https://www.treesearch.fs.fed.us/pubs/51058

https://www.treesearch.fs.fed.us/pubs/51076

https://www.treesearch.fs.fed.us/pubs/52016

https://www.treesearch.fs.fed.us/pubs/52017

https://www.treesearch.fs.fed.us/pubs/52019

https://www.treesearch.fs.fed.us/pubs/52070

https://www.treesearch.fs.fed.us/pubs/52089

https://www.treesearch.fs.fed.us/pubs/52214

https://www.treesearch.fs.fed.us/pubs/52214

https://www.treesearch.fs.fed.us/pubs/52215

https://www.treesearch.fs.fed.us/pubs/52223

https://www.treesearch.fs.fed.us/pubs/52225

https://www.treesearch.fs.fed.us/pubs/52233

https://www.treesearch.fs.fed.us/pubs/52237

https://www.treesearch.fs.fed.us/pubs/52239

https://www.treesearch.fs.fed.us/pubs/52320

https://www.treesearch.fs.fed.us/pubs/52322

https://www.treesearch.fs.fed.us/pubs/52326

https://www.treesearch.fs.fed.us/pubs/52360

https://www.treesearch.fs.fed.us/pubs/52362

https://www.treesearch.fs.fed.us/pubs/52364

https://www.treesearch.fs.fed.us/pubs/52469

https://www.treesearch.fs.fed.us/pubs/52469

https://www.treesearch.fs.fed.us/pubs/52500

https://www.treesearch.fs.fed.us/pubs/52505

https://www.treesearch.fs.fed.us/pubs/52506

https://www.treesearch.fs.fed.us/pubs/52509

https://www.treesearch.fs.fed.us/pubs/52510

https://www.treesearch.fs.fed.us/pubs/52511

https://www.treesearch.fs.fed.us/pubs/52512

https://www.treesearch.fs.fed.us/pubs/52535

https://www.treesearch.fs.fed.us/pubs/52558

https://www.treesearch.fs.fed.us/pubs/52559

https://www.treesearch.fs.fed.us/pubs/52562

https://www.treesearch.fs.fed.us/pubs/52563

https://www.treesearch.fs.fed.us/pubs/52564

https://www.treesearch.fs.fed.us/pubs/52639

https://www.treesearch.fs.fed.us/pubs/52640

https://www.treesearch.fs.fed.us/pubs/53060

https://www.treesearch.fs.fed.us/pubs/53067

https://www.treesearch.fs.fed.us/pubs/53106

https://www.treesearch.fs.fed.us/pubs/53108

https://www.treesearch.fs.fed.us/pubs/53109

https://www.treesearch.fs.fed.us/pubs/53110

https://www.treesearch.fs.fed.us/pubs/53111

https://www.treesearch.fs.fed.us/pubs/53112

https://www.treesearch.fs.fed.us/pubs/53120

https://www.treesearch.fs.fed.us/pubs/53122

https://www.treesearch.fs.fed.us/pubs/53123

https://www.treesearch.fs.fed.us/pubs/53124

https://www.treesearch.fs.fed.us/pubs/53125

https://www.treesearch.fs.fed.us/pubs/53126

https://www.treesearch.fs.fed.us/pubs/53127

https://www.treesearch.fs.fed.us/pubs/53128

https://www.treesearch.fs.fed.us/pubs/53129

https://www.treesearch.fs.fed.us/pubs/53130

https://www.treesearch.fs.fed.us/pubs/53131

https://www.treesearch.fs.fed.us/pubs/53132

https://www.treesearch.fs.fed.us/pubs/53133

https://www.treesearch.fs.fed.us/pubs/53134

https://www.treesearch.fs.fed.us/pubs/53136

https://www.treesearch.fs.fed.us/pubs/53137

https://www.treesearch.fs.fed.us/pubs/53138

https://www.treesearch.fs.fed.us/pubs/53139

https://www.treesearch.fs.fed.us/pubs/53140

https://www.treesearch.fs.fed.us/pubs/53141

https://www.treesearch.fs.fed.us/pubs/53142

https://www.treesearch.fs.fed.us/pubs/53143

https://www.treesearch.fs.fed.us/pubs/53144

https://www.treesearch.fs.fed.us/pubs/53146

https://www.treesearch.fs.fed.us/pubs/53147

https://www.treesearch.fs.fed.us/pubs/53148

https://www.treesearch.fs.fed.us/pubs/53156

https://www.treesearch.fs.fed.us/pubs/53157

https://www.treesearch.fs.fed.us/pubs/53158

https://www.treesearch.fs.fed.us/pubs/53160

https://www.treesearch.fs.fed.us/pubs/53161

https://www.treesearch.fs.fed.us/pubs/53162

https://www.treesearch.fs.fed.us/pubs/53162

https://www.treesearch.fs.fed.us/pubs/53162

https://www.treesearch.fs.fed.us/pubs/53163

https://www.treesearch.fs.fed.us/pubs/53165

https://www.treesearch.fs.fed.us/pubs/53166

https://www.treesearch.fs.fed.us/pubs/53167

https://www.treesearch.fs.fed.us/pubs/53169

https://www.treesearch.fs.fed.us/pubs/53170

https://www.treesearch.fs.fed.us/pubs/53175

https://www.treesearch.fs.fed.us/pubs/53176

https://www.treesearch.fs.fed.us/pubs/53187

https://www.treesearch.fs.fed.us/pubs/53244

https://www.treesearch.fs.fed.us/pubs/53245

https://www.treesearch.fs.fed.us/pubs/53246

https://www.treesearch.fs.fed.us/pubs/53247

https://www.treesearch.fs.fed.us/pubs/53248

https://www.treesearch.fs.fed.us/pubs/53249

https://www.treesearch.fs.fed.us/pubs/53356

https://www.treesearch.fs.fed.us/pubs/53379

https://www.treesearch.fs.fed.us/pubs/53385

https://www.treesearch.fs.fed.us/pubs/53641

https://www.treesearch.fs.fed.us/pubs/53642

https://www.treesearch.fs.fed.us/pubs/53644

https://www.treesearch.fs.fed.us/pubs/53646

https://www.treesearch.fs.fed.us/pubs/53647

https://www.treesearch.fs.fed.us/pubs/53647

https://www.treesearch.fs.fed.us/pubs/53651

https://www.treesearch.fs.fed.us/pubs/53708

https://www.treesearch.fs.fed.us/pubs/53841

https://www.treesearch.fs.fed.us/pubs/53841

https://www.treesearch.fs.fed.us/pubs/53842

Copy and paste these to the online tool for "Find and Replace" used earlier (textmechanic.com)

"FInd" the string "https://www.treesearch.fs.fed.us/pubs/" and "Replace" with "nothing" (i.e., no characters, nothing, zilch, nada, not even white space). The goal here is to get the TreeSearch ID all by itself.

Create a new column, "TreeSearch_ID" and paste all the TreeSearch ID’s into that column (select the first cell in the column where you wish to put this data). Double check to be sure the TreeSearch ID code matches the TreeSearch URL/

Create a new tab in your spreadsheet, "merge."

In Columnn B, paste your TreeSearch IDs.

IN column A, paste the following:

https://data.fs.usda.gov/research/services/westernstubservices/productsservicesentry?product_id=&treesearch_id=52214

Propagate that down the entire column (easiest way is to select the right lower corner of the cell, until a ‘+’ appears, then drag it down.

Now you need to merge the two columns into a single, connected URL string.

Goal:

https://data.fs.usda.gov/research/services/westernstubservices/productsservicesentry?product_id=&treesearch_id= 53842

into

https://data.fs.usda.gov/research/services/westernstubservices/productsservicesentry?product_id=&treesearch_id=53842

Return to the online text editing tool (textmechanic.com) to "Find and Replace."

This time, you are "Finding" the blank space, and "replacing" with "nothing" (again, nothing, nada, zilch to eliminate any and all blank space betweeen the TreeSearch ID in COlumn B and the URL string in Column A).

Copy one of the blank spaces (and only the blank spaces) from between id= and the TreeSearch ID. Paste that into the "find" option. It is very likely five single spaces (a tab).

In the "Replace with" box, delete everything so it’s "nada, zilch, nothing."

Execute.

Copy and paste the result back to your "merge" spreadsheet in column C if you wish. Check again to be sure you did not miss anything (1:1 match between source data and new URL strings).

Go back to Sheet1 in your pub_update workbook.

Add a new column for "TreeSearch_XML"

Paste your new URL strings there.

Double check again to be sure there is a 1:1 match from original data to new data.

Save the spreadsheet.

Back in FireFox, use the "Open Multiple URLs" tab and paste in your list of TreeSearch XML.

Wait for the URLS to load.

Scroll your tabs all the way to the left and start at the beginning. You are looking for the Digital Object Identifier.

You can expedite this by searching for "DOI" in Firefox "Find" mode. (Ctrl + F)

Systematically copy the DOI and paste it into your spreadsheet.

If not available, write, NA and move on to the next one.

Clean the list to remove any "http://dx.doi.org/" – the goal is to have the DOI alone.

The end result is a list of Digital Object Identifiers. IN this example, I obtained

IN this case, only 96 out of the total 178 had a DOI (from my method). 52 were coded "NA."

.

http://tdmsupport.crossref.org/researchers/

Example;

http://dx.doi.org/10.1016/j.jenvman.2015.12.017

http://dx.doi.org/10.1016/j.landurbplan.2015.11.007

http://dx.doi.org/10.1071/WF14166

http://dx.doi.org/10.1071/WF14170

http://dx.doi.org/10.1071/WF15092

Metadata search via crossref:

http://search.crossref.org/?q=10.1071%2FWF15092#

Metadata as JSON

https://api.crossref.org/v1/works/http://dx.doi.org/10.4996/fireecology.1202001

https://blog.mendeley.com/2011/03/21/7-ways-to-add-documents-to-mendeley/

Capture: Capture Reference

To install the Capture tool, just drag the Capture Reference button to your Bookmarks bar (also known as "Favorites Bar" or "Bookmarks Toolbar"). In some browsers, you may need to right-click and select "Add to Favorites" or "Bookmark This Link."

To use it, browse to a page you like and click the Capture Reference button in the Bookmarks bar. The Capture Reference window will open. Follow the instructions in the window.

View Bookmarks Bar

https://www.mendeley.com/download-mendeley-desktop/

https://blog.mendeley.com/2011/03/21/7-ways-to-add-documents-to-mendeley/

http://service.elsevier.com/app/home/supporthub/mendeley/

I think for now, install the Firefox web app for mendeley, then add them all.

Make a new sheet, call it "doi merge."

In column A, enter "http://doi.org/"

In column B, enter the list of DOI.

Propagate Column A to match Column B

Unite two columns using process described already.

Maybe "CiteULike" has some kind of tool?

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RITS_2016_PNW_Pubs_Copy_Pasted-v02.xlsx

Questions re: pre-approved software

Hi James,

Any thought on pre-approval of mendeley?

https://www.mendeley.com/download-mendeley-desktop/

I noticed it is not here:

http://fsweb.wo.fs.fed.us/cio/strategic-planning-information-management-and-architecture/documents/Pre-Approved_Software_20170301.pdf

Thanks,

Tanner

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Archiving FS Software?

Some ideas on archiving Forest Service software as digital research output.

From: Jessel, Tanner – FS
Sent: Friday, April 14, 2017 11:50 AM
To: Pye, John -FS < >
Subject: Archiving FS Software?

Hi John,

Because my background is library science and data archival, I am very interested in the long-term archival of PNW research products.

While at PNW, I have noticed that our researchers produce a notable amount of computer software.

I suppose that includes web software along with downloadable executable files or “.msi” files, or extensions to ArcGIS.

I wonder if you happen to know if the Research Data Archive would be able to support archival of executable files, or other computer code, to provide a stable long-term “home” for executable research output?

If the RDA is not able to host code or executable files, I wanted to point out two possible ideas:

1. A Forest Service Institutional Repository for Code on FigShare:

a. https://figshare.com/search?q=software&quick=1

2. A Forest Service GitHub, similar to the GSA GitHub: https://github.com/GSA and https://github.com/usgs

A related problem is that the native environment for Forest Service software tools regularly disappears over time.

I read in tech news that Windows Vista would no longer be supported – it brings up an interesting question of emulators. It seems like, over time, a lot of our software tools will be rendered inoperable as their native operating systems and environments are deprecated.

There’s a lot of interest in software curation / native OS emulation / virtualization in the Library Sciences.

A presentation on it here, from Yale University Dean of University Libraries:

https://www.slideshare.net/cmkeithw/software-curation-as-a-digital-preservation-service

· http://blogs.loc.gov/digitalpreservation/2014/08/emulation-as-a-service-eaas-at-yale-university-library/

· https://olivearchive.org/

Thanks for any info on if RDA could function as a long-term home for either code or executable files. I suppose the alternative ideas, if RDA isn’t set up to work that way, are just thoughts to hold on to.

-Tanner

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