Elephant seals!

Spent the morning on Morro Bay watching a raft of sea otters, then the better part of midday watching elephant seals on the beach. Two large males are up on the beach with several younger males trying to act the part...

Sent from my Windows Mobile® phone.

Fresh coastal air

As the fall break is upon CSUF, I took the family on a drive up the central coast to get some fresh and cooler air than we have had in Fullerton.  We headed north to Morro Bay after work yesterday and spent today between Morro Bay, Big Sur, and Monterey Bay.  It was gray and rainy, but a nice change of pace from the long lasting east winds and high pressure over the Southland.  It feels great to get some fresh cool air, some rain, and some open road.  We saw one sea otter near Cambria, then saw a large group of elephant seals at a haul out near Hearst Castle. I have included a picture of a large male here. We then spent the afternoon at the Monterey Bay Aquarium.  It has been some time, but in graduate school I did a few projects that focused on yellowfin tunas.  While my wife was in vet school, we did a project sampling juvenile yellowfin tuna dockside in Louisiana for mercury levels.  I also spent a few days trying to track yellowfin tunas around oil platforms in the Gulf of Mexico. We successfully tracked one fish for about an hour or so in 2004.  Those tracking data were included in Dr. Greg Skomal's dissertation work at Boston University.  The aquarium has several yellowfin tuna in their outer bay exhibit. That was very cool to see.

Testing a mobile post

Hello everyone. Given the mobile nature of much of our work in SEER Lab, I am larning to blog from my mobile. This is a test post. I use a mobile phone running Windows Mobile 6.1 and even have a GPS and ArcPad loaded so mobile blogging falls in perfectly with my approach to travel and travel gadgets. The photo quality was poor, so I removed it, but the mobile approach does allow photo additions.

Working in Big Sky country

The trip to Bozeman was quick and we had a great deal of work to accomplish. In addition to field sampling four bull elk and a deer, we also had several meetings to discuss outbreak control strategies and discuss future steps on disease control and surveillance. It was a very successful trip.  Additionally, I was also able to introduce my Geography 327: Geography of Health to disease sampling and field work via my webcam on cell phone.  I also taught my Geography 485: GIS for Public Health class via a webcam and an online slide show of field sampling.  The photos here show how class was taught from the back of a truck, sampling a dead elk, mapping out case locations with a Trimble PDA running ArcPad, and some live bison on the range.  There is more information on the outbreak at promed mail archive number 20080802.2366 if you are interested.

Outbreak investigations are always interesting.  They are a combination of field work (like ecology, biology, pathology, and epidemiology) and working group meetings.  Field research on outbreaks is used in a number of ways. In the SEER Lab, these data are used to expand our knowledge of the ecology of disease - or how it works across spatial scales.  Spatial data will be used to improve my ecological niche models defining disease distribution and aim to improve those models. We use those to inform regions or states of potential areas where outbreaks might be more likely than others.  We also use field data to better understand the distribution of cases and aim to determine how outbreaks start, perpetuate, and eventually end.  Working group meetings are where stakeholders share knowledge, concerns, and ideas of how to better manage wildlife and livestock in disease areas, prepare for future outbreaks, and determine best courses of action or policy to insure domestic and wild herd health along with human public health in the event of future outbreaks.

The outbreak visited in south Texas back in July/August (see earlier SEER Lab Travel Log blog entries) was only in domestic cattle and was a much smaller number (though it is likely there were some deer affected).  The goal of SEER Lab is to understand the biogeographic similarities and differences in environment, possible vectors (e.g. flies), wildlife species, and herd management that serve as driving mechanisms for outbreaks in different regions from south Texas to the northern states and Canada, and across Central Asia.

Big Sky...

I am back on the road again. This week I am in Bozeman, MT investigating a large outbreak in wildlife. I am here through the end of the week working with a local wildlife veterinarian and his colleagues. Today I arrived in Bozeman around 415 pm. I was supposed to get in at noon, but a mechanical problem kept us grounded in the OC long enough to miss my connection in Salt Lake City, UT. I had to spend about 3 1/2 hours in UT, but used the time to get caught up on some lecture notes (yes... school is back in session too) and some writing. In addition to the field work we have been doing this summer, I am in the final throws of a paper for a NATO Science for Peace and Security conference that I attended in Tbilisi, Georgia earlier in the summer. I have been developing models of how disease distributions might differ from the present day in the year 2050, using some data from the Inter-governmental Panel on Climate Change and ecological niche modeling.

Upon arriving, the wildlife veterinarian was very helpful and quick to share details of the situation. I was given a series of maps and some environmental data on the ranch we will be visiting and we were able to compare this to some of the ecological niche modeling I have done in the past for the U.S.

The photos here show some of the gear I am preparing for tomorrow's field investigation and some of the documentation we have been reviewing this evening, and a view of the "Big Sky".

Back on the road...

After some downtime with the family and recovery from a nasty outer ear infection (could not resist a way-to-hot freshwater pool in Texas on our lab trip - see previous posts), I am back on the road this Monday thru Thursday for work on some of our international research projects. The flight in was an easy direct flight from LAX to Washington Dulles followed by a quick midnight cab ride to the hotel. Traveling for the SEER Lab is full of planes, trains, autos, 4x4s, and even boats and ATV's (sometimes). This shot is of the elevated bus ride from our terminal to the baggage claim area. I travel lite, so no baggage for me. The other photo is the computer setup... add it to the list of locations we setup shop (See previous blog).

down time...

Last week I took my family on a camping trip to King's Canyon National Park in the Sierras.  It was a much needed break and the park is absolutely beautiful.  My daughter is almost 1 (a few weeks to go) and she loved every bit of it. First sleep over in a tent for her, first cave, first large waterfalls, first huge mountains, first hike in a thunderstorm, first rattlesnake, first black bear... it was an awesome week.

Back at it with travel this week. Headed to DC for a few days for project meetings and some US-based research on the Azerbaijan projects that Ian blogs about (http://seerlab-azerbaijan.blogspot.com).  If I get into DC proper, I will post some photos.

Soil sampling

Saturday was our final day of field work on this (short) trip to south Texas. In addition to sampling vegetation and ground truthing the t-cap data, we needed to collect soil samples from some potholes in the northern extent of our current study site. In the past we have used two soil sample site selection methods, regular grid sampling and regular-interval line transects, to delineate "edges" of potholes. For this trip we used a line transect to collect 20 soil samples from a northern pothole in Jim Hogg County. In this photo Ann is collecting a soil sample that will be processed for several key minerals back at the soils lab at Louisiana State University (we sent them home with Martin).

Setting up shop

One of the exciting parts of field work is "setting up shop", or finding empty space in the brush, in the truck, or in the bunk house/tack room to scratch out a corner setup a computer to prep or backup field data.

This week we used the Jeep Liberty, the horse tackle room, and the brush to setup shop and move data between the PDAs and the laptops.

While not ergonomic, an uncomfortable round of data prep in the field beats a day in the AC and white lights of the lab!

Ground truthing t-cap images

Friday was day 2 in field in South Texas. We returned to a large pothole that Martin and I have been sampling since 2003. In 2004 we did some extensive soil sampling to evaluate the soil conditions in and around the pothole and used those data to determine the "edge" of the pothole. During Friday's efforts, we were attempting to determine if particular plant species delineate the same "edge". As could be expected, the plant distribution is more complex than the soil distribution, but we do have some key plants that indicate "in" or "out" of the pothole.

In addition to some plant sampling, we also used the GPS and laptop to identify potential potholes from the t-cap images and then used some four-wheel drive and some hiking to identify and additional four potholes that we had not identified or sampled in the past. By the end of the day we were batting 1000 on identifying potholes from the imagery and confirming them with field searches.

The photo included with this post shows Kim and Ann identifying plant species at sampling sites. Sampling sites were randomly selected using a psuedo-random sampler in the Hawth's tools extension in ArcGIS 9.2.

animals in potholes

As part of our sampling, we also look for signs of animal deaths in potholes. When we find bones or animal remains, we map the position of the sample, then submit the sample to our diagnostics laboratory collaborators to test for evidence of disease. Martin found one of two deer skulls today, Kim found the second.

PDA-GIS field methods

As part of our field sampling we load satellite imagery and develop random sampling points to the PDA through a laptop. Pictured here is Ian and I working to create a random sample that is specific to our field location for the day. We setup shop in a spot of shade so we could see our monitor on the laptop. As part of this work, we are using the new Magellan Mobile Mapper 6 loaded with ArcPad 7.1. Once we have a sampling scheme setup, we navigate to each site with the GPS, then mark our proximity to the random sample we are navigating to, and capture our data attributes. The second photo shows Ian at work navigating to a sampling site.

Ground Truth... notes from the field

Hello from the field. I am traveling this week with Kim Pham, Ian Kracalik, and Ann Espejo. Kim and Ian are masters students in Geography and Ann is an undergraduate student. We are also joined by Dr. Martin Hugh-Jones, emeritus professor, from Louisiana State University. This week we are working from South Texas on ranches near Falfurrias and Hebronville to continue our work on the ecology of zoonotic diseases. Specifically, we are working to ground truth some remote sensing work we have developed. We have been working with Landsat 7 ETM+ and Landsat 5 satellite images to identify a unique habitat known as coastal potholes. These potholes are low lying depressions that collect water, soil, and organic material and provide great habitat for deer and cattle to dodge the heat. Martin and I have been working since 2003 to identify these habitats and to develop a methodology to delineate them from remotely sensed images. As part of our efforts, Martin and I have returned to several key potholes repeatedly to collect soil samples, measure plant abundance, and evaluate animal usage of these habitats. As part of our efforts, we have been using the tassel-cap transformation on Landsat images and using these outputs to identify known potholes and then estimate locations of unknown potholes. We couple this remote sensing effort with field data and handheld PDA-GIS (ArcPad and various PDA technologies) to travel to estimated potholes and confirm their presence in the imagery.

Since the fall of 2007, Kim and I have been expanding the research methodology to include more significant plant taxonomy of species Martin and I have used to delineate potholes and the inclusion of NDVI in addition to tassel-cap. Additionally, Kim and I have working to describe the seasonality of potholes from the t-cap analyses using images from multiple seasons across a two-year period.

This week we are here to ground truth our more recent efforts and expand our plant sampling. As part of this, Ian and Ann have joined our research team. Ian also has experience with handheld PDA technologies and is working closely with me to capture field data and navigate across the imagery. As part of this Ann is joining us to learn some of our field methodology and explore biogeography and medical geography in a single trip.