Erik Barry Erhardt, PhD

Laurel Goode, Erik Erhardt, Louis Santiago, and Michael Allen.
δ13C of soluble sugars in Tillandsia epiphytes vary in response to shifts in habitat.
Oecologia, Physiological ecology section, 2010.

I met Laurel at SIRFER 2008 where we enjoyed a wide range of stable isotope lectures and lab experience. She first used my software, SISUS, to estimate the proportion of C3 vs CAM photosynthesis of epiphytes. Our work and friendship led to the collaboration where we thought about and developed a model for the environmental factors affecting the phothsynthetic pathways of the species studied.

Abstract

We studied carbon stable isotopic composition (δ13C) of bulk leaf tissue and extracted sugars of four epiphytic Tillandsia species to investigate flexibility in the use of crassulacean acid metabolism (CAM) and C3 photosynthetic pathways. Plants growing in two seasonally-dry tropical forest reserves in Mexico that differ in annual precipitation were measured during wet and dry seasons, and among secondary, mature, and wetland forest types within each site. Dry season sugars were more enriched in 13C than wet season sugars, but there was no seasonal difference in bulk tissues. Bulk tissue δ13C differed by species and by forest type, with values from open-canopied wetlands more enriched in 13C than mature or secondary forest types. The shifts within forest habitat were related to temporal and spatial changes in vapour pressure deficits (VPD). Modeling results estimate a possible 4% increase in the proportional contribution of the C3 pathway during the wet season, emphasizing that any seasonal or habitat-mediated variation in photosynthetic pathway appears to be quite moderate and within the range of isotopic effects caused by variation in stomatal conductance during assimilation through the C3 pathway and environmental variation in VPD. Carbon isotopic analysis of sugars together with bulk leaf tissue offer a useful approach for incorporating short- and long-term measurements of carbon isotope discrimination during photosynthesis.

Statistics, stable isotopes

Wednesday, August 12th, 2009 exceeded my expectations in so many ways.  I was really touched by having so many people in attendance for my dissertation defense.  Friends and professors from math & stat, biology, and other departments, collaborators from the medical campus and from consulting outside the university, and my mom and brother.  About 25-30 in all.

My advisor, Edward Bedrick, provided a wonderful introduction that reminded me of the many ways I’ve connected with the UNM community: teaching (and awards), research assistantships (and publications), statistics department consultant, collaborations, and unicycling around campus those first few years.

I was generally happy with my presentation and was grateful that Ed reminded me occasionally of points that I wanted to make but had forgotten to mention.  He was also my champion whenever I tried to sell myself short, interjecting and saying that a particular point I was glossing over is nontrivial in theory and application.  I had some positive feedback and am learning how to give better talks.

My committee’s questions really helped me feel more like a peer, asking questions with the expectation that I might provide insight on a topic.  They never asked a question with the goal to stump me or make me feel small.  I felt supported, respected, encouraged, and welcomed into PhD family.

What next?  I’m now a postdoc at the Mind Research Network on the UNM campus in Albuquerque doing modeling for fMRI brain imaging data, see previous post.  I’m completing my dissertation to submit to the university, writing papers from the dissertation, and organizing work on my other collaborations.  These next couple years are going to challenging and exciting, frustrating and daunting, engaging and inspiring, and I’d better also say peaceful and tranquil so my mom thinks I’m getting some rest, too.  Carpe data!

Research

Dissertation defense for Erik Barry Erhardt, PhD candidate in Statistics
Wednesday, August 12th at 10am in Humanities 428
University of New Mexico

Title: Stable Isotope Sourcing using Sampling

Abstract:

Stable isotope sourcing is used to estimate proportional contributions of sources to a mixture, such as in the analysis of animal diets, plant nutrient use, geochemistry, pollution, and forensics. We focus on animal ecology because of the particular complexities due to the process of digestion and assimilation. Parameter estimation has been a challenge because there are often many sources and few isotopes leading to an underconstrained linear system for the diet probability vector. This dissertation off ers three primary contributions to the mixing model community. (1) We detail and provide an R implementation of a better algorithm (SISUS) for representing possible solutions in the underconstrained case (many sources, few isotopes) when no variance is considered (Phillips and Gregg, 2003). (2) We provide general methods for performing frequentist estimation in the perfectly-constrained case using the delta method and the bootstrap, which extends previous work applying the delta method to two- and three-source problems (Phillips and Gregg, 2001). (3) We propose two Bayesian models, the implicit representation model estimating the population mean diet through the mean mixture isotope ratio, and the explicit representation model estimating the population mean diet through mixture-specific diets given individual isotope ratios. Secondary contributions include (4) estimation using summaries from the literature in lieu of observation-level data, (5) multiple methods for incorporating isotope ratio discrimination (fractionation) in the analysis, (6) the use of measurement error to account for and partition more uncertainty, (7) estimation improvements by pooling multiple estimates, and (8) detailing scenarios when one model is preferred over another. We show that the Bayesian explicit representation model provides more precise diet estimates than other models when measurement error is small and informed by the necessary calibration measurements.

Research

Seymour Grufferman, Frederick Ruymann, Simona Ognjanovic, Erik B. Erhardt, and Harold M. Maurer.
Prenatal X-ray Exposure and Rhabdomyosarcoma in Children: A Report from the Children’s Oncology Group.  Cancer Epidemiology Biomarkers & Prevention. April 2009, 18(4), OF1–6. [pdf]

This is the first in a series of papers that will be the result of my research assistantship Fall 2005 — Spring 2008 with Seymour Grufferman, M.D., Dr. P.H. and Deirdre A. Hill, Ph.D., M.P.H. at the Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131, USA.  More results are likely to come from this rich dataset.

Research

On Jan 20th, 2009, I joined the Medical Image Analysis Laboratory (MIALab) as a research assistant (RA) at the MIND institute at UNM.  This position will transition to a 2-3 year postdoc upon the completion of my PhD this May.

Vince Calhoun, Edward Bedrick (my stat advisor), Jeremy Bockholt, and I compose the Biostatistics & NeuroInformatics Core (STATNI) on UNM’s Center of Biomedical Research Excellence (COBRE) grant funded by the National Center for Research Resources (NCRR), a part of the National Institutes of Health (NIH).  STATNI serves as a centralized resource for biostatistical consulting for a number of scientific projects. My role will be in the development of statistical methods and programming numerical and statistical methods to address the aims of the projects.  Specifically, the development of a Bayesian ICA model for fMRI data.

There are five aims to the project that will ultimately extend the ability to incorporate prior information to move beyond the semi-blind ICA approach. [from the project summary] First, we will extend our semi-blind ICA (sbICA) framework to provide a general framework for incorporating prior information from multiple spatial and temporal sources. In the second aim we will focus upon statistical inference and develop a framework for integrating the relevant functional components. In the third aim, we will validate the algorithms in aims 1 and 2, including using fMRI data collected on multiple days from a variety of paradigms. In this aim we develop a decision mechanism for selecting the best combination of methods given a particular problem. For the fourth aim, we will apply our methods to data collected during four well-studied paradigms in healthy controls and patients with schizophrenia. Our final aim involves the continuing development of our GIFT toolbox, and incorporation of the above algorithms, constraint selection mechanisms, and visual interfaces into the software. The successful completion of this research will provide a powerful set of tools for the research community to increase the sensitivity and specificity of BOLD analysis methods by drawing upon the strengths of both model-based and data-driven approaches. These tools will also provide a way to study the inter-relationship among functional networks in a flexible manner.

This is an ideal position for me because the modeling is similar to work I have done in my dissertation, I continue to work closely with my advisor, Ed, who I continue to learn so much from, I get to learn and work with Vince who has many ideas and is very prolific, and all of this in the hot area of fMRI.  I also have family and friends in Albuquerque who I want to stay close with for a little longer and this position allows me to stay put.

MIND

Christopher P. Bickford, Nate G. Mcdowell, Erik Barry Erhardt, Heath H. Powers, David T. Hanson. (2009)
“High frequency field measurements of diurnal carbon isotope discrimination and internal conductance in a semi-arid species, Juniperus monosperma“.
Plant, Cell & Environment, In print (1/28/09).

Chris Bickford, PhD candidate UNM Biology, and I met when we attended Iso-Camp at Jim Ehleringer’s lab at U Utah Summer 2008.  On the flight home we started discussing a challenge he was facing in his first of three dissertation papers. He studies details of plant photosynthesis.  He had complicated expressions for leaf carbon isotope discrimination and internal conductance based on CO concentrations of CO isotopologues and . He needed to propigate the variation of the CO measurements into his variables of interest, and .  He also needed to compare his accurate and precise measurements using tunable diode laser spectroscopy (TDL) to predictions from three models.

There were a number of statistical issues.  One was how to make model and observation comparisons.  I suggested using RMSE since it includes both variance and bias in the single measurement.  The main issue was the incorporation of variation from the CO measurements into the quantities of interest.  The bootstrap allowed us to do this.  There were a number of programming sessions in R to write functions and scripts to do all the calculations, create plots, output spreadsheets of results, and so on.  Chris has become a convert from Excel to R over the course of this project.  These methods implemented on this paper will likely flow into later pubs for both Chris and Dave.

Chris has taken a postdoc in New Zealand, where he and his wife, Karen, will spend the next two years with their dog.  He defends his dissertation on April 13th.

stable isotopes

I developed a solitaire game for pool (pocket billiards) that stresses the importance of making every shot count and developing your balls-per-inning potential for those of us who often run between 2 and 10 balls, based on straight pool.  I call it “Penalized-x”, where “Penalized-5″ would specify 5 penalty balls. The rules:

1. Rack all 15 in the standard way, start with cue on the head spot.
2. Choose a number of penalty balls, a number of balls from 1 to 14.
3. All shots except the break must be made with the intention of sinking a called ball in a called pocket; shots taken explicitly to spread the balls are not allowed.
4. On any miss, foul, or scratch return the number of penalty balls to the table, spotted in the standard way starting at the foot spot along the foot line to the foot of the table, and continuing at the foot spot toward the head of the table.
5. On a scratch, additionally, the cue is placed on the head spot if unobstructed, else on the center spot if unobstructed, else in the kitchen.
6. The game ends when the last ball is potted with a legal stroke.
7. The game is scored by the two numbers balls/innings, which also gives balls per inning. For example, 78/23=3.39 indicates 78 balls potted in 23 innings for 3.39 balls per inning.

Leave a comment to let me know what you think, or if you have any suggestions for improvement.
My games so far:

Penalized-5 (date - balls/innings=bpi)

1. 20081230 - 78/23=3.39, end run 9,11
2. 20081231 - 45/12=3.75, end run 15
3. 20090101 - 71/21=3.38, end run 15
4. 20090101 - 61/15=4.07, end run 15
5. 20090102 - 270/63=4.28, end run 7,13 (made it to 1 ball 3 times)

pool

I’m starting to dance again, after developing (2004ish) and having surgery (Dec 2006) to remove a Morton’s Neuroma in my left foot from dancing in beautiful shoes that were too narrow; it’s hard to find dance shoes in a 11-4E. To celebrate, here’s a contra I wrote some years ago, which I first called at CCDS 2009.

The Calamitous Milkcrate Caper

by Erik B. Erhardt, 2003.05.27

Duple Improper Contra Dance

[Pulses Call]
A1:
4 Circle Left 1/2
4 Gent Roll Partner [Lady] Left into (no sashay, Gents are anchored in place)
4 Gents Chain across by the Right [hand] (the Gents are doing a Ladies chain)
4 Ladies Courtesy turn Gents (give Left hands, wheel around)
A2:
4 Circle Right 1/2
4 Lady Roll Partner [Gent] Right into (no sashay, Ladies are anchored in place)
8 Ladies Left shoulder 1/2 Hay
B1: (the tease)
6 Gypsy Partner 3/4 around (until the gents are facing in)
2 Gents cross set (by right shoulders) into
8 Swing Neighbor on Lady’s side
B2:
4 Ring Balance
4 Active Lady California twirl Partner/Gent (Lady lift right hand, gent turn under, and pull into a swing)
8 Actives Swing
while Inactives cast alone over outside shoulder

[can alternate actives and inactives role in B2 if long sets and very sharp dancers, caller may need to cue actives/inactives for swing throughout]

Dance Notes:

• This dance was written with gender role reversal in mind. It’s about time the guys get the dance action! Also, if the gypsy is done meaningfully, it can be a real tease.
• It’s probably worth a little extra instruction to get the Gents Chain across correct. Most people only dance one gender role. As such, they have difficulty when called upon to reverse roles. I suggest two walk-thrus of the Gents chain across. The first one suggest the traditional courtesy turn with the right hands on the waist/lower back. The second one suggest an underarm twirl. This will give the dancers a wider vocabulary of moves.
• Also, I would suggest that if the man is much taller than the lady, that they resort to the traditional courtesy turn rather than the underarm twirl to avoid injury. In this case there is a nice “whip” twirl where, if they take hands in front for the turn, at the end the lady can whip the guy for an unspotted spin (guy spins counter-clockwise) at the end. More advanced dancers will find this on their own.
• 12/30/09 - Made two corrections (B1 gypsy 1/2, B2 Actives only Cali turn) and expanded explanations.

dance

In high school I mostly played guitar, and in college I mostly composed music on the computer. Here’s a selection of that work.

Liquid Mazes, 1993 (High school)

I wrote (most) and recorded these songs while in high school. I played guitar, was significantly influenced by Steve Vai, Joe Satriani, and JS Bach. “Joy” and “Satch” are probably my favorites. My mom was holding a dieing tape recording the the audience for “Satch”, which is why the speed and pitch both increase slightly over the course of the recording.

Computer Music, college (1995-1997)

Encore music composing software seemed pretty advanced, even over ten years ago, and enabled me to compose some simple multipart pieces. You can listen quickly from the “mid” link (for midi) and see the notation using “ps” or “pdf”. The first two and the last are probably my favorite.

music

C MPI implementation of waves equation on 16 processors, init + 10 time steps.

Thanks to Matthew Bohnsack for setting my site up on wordpress. Matt and I worked together on projects in CS 442 Introduction to Parallel Processing in Fall 2006.

He’s hosted my site since April, 2007, and there have been terrific benefits. First, the server is beautifully configured and fast, and he’s given me plenty of space. Working with him has allowed me to provide my SISUS software prototype, which is an R package which I haven’t released, yet. He discusses his implementation of the software needed in his blog post. He is quick to respond, works meticulously, and understands the big picture as well as the individual pixels.

Fun