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Geoffrey L. Johnston

Ph.D. Student in Sustainable Development

School of International and Public Affairs/Earth Institute

Columbia University


Email: glj2108 (at) columbia.edu                    My résuméResume


Current Research         Blog         Previous Publications

Images        Important Links         Files


Introduction
:

First, hello and welcome.  My name is Geoff; I am currently a Ph.D. student in the Sustainable Development program at Columbia University.  If you are interested in the program, you can find more information here and here

A little background: I graduated from the University of Notre Dame, summa cum laude, in 2005 with a Bachelor of Science in Honors Mathematics and a Bachelor of Arts in Philosophy.  From there I taught in a Mississippi high school for two years as a member of Teach for America and then a further year in a Cleveland charter school (5th and 6th grade math and science).

In the course of my studies, I researched various programs designed to promote holistic human development, eventually discovering the program in which I am currently enrolled.  Now I am here in New York, researching, studying, and hopefully helping. 



Research Interests:


My primary research interest is learning more about poverty: its causes, its effects, and its cures.  I am also interested in complex systems and their usefulness in describing natural and human-engineered systems.

In pursuit of this broader agenda, I am currently working on a few specific projects. 

The first project that I am working on is building mathematical models of malaria transmission.  The purpose of these models is to help public health agencies better predict where and when malarial epidemics will arise, as well as provide likely patterns of drug resistance development.  My advisors on this project are David Fidock, a microbiologist at Columbia (Fidock Lab), and David Smith, a malaria modeler at Resources for the Future (RFF) as well as the Emerging Pathogens Institute at the University of Florida (EPI).  This project was the basis for my successful research proposal for the NSF Graduate Research Fellowship.

I am also working on is quantifying the effectiveness of a variety of development interventions currently being employed in the Millennium Village Project (MVP).  Within the development community today there is great debate over the value of foreign aid, with positions ranging from the belief that aid does more harm than good to the belief that aid is necessary for development.  I hope to work with the MVP team to rigorously quantify the impact that various interventions are having and their cost-effectiveness.   More data will provide macroeconomists and other aid researchers and practitioners with inputs to support or falsify their theories.



Current Research:

There are there major projects that I am working on relating to the modeling of malaria.  The first project utilizes clinical data to model the progression of malaria within a host.  We simulate treating these hosts with different antimalarial drugs in order to predict how the drugs' different modes of action will affect transmission.  I am building the code in MATLAB (+1000 lines and going strong) and we are nearing completion. 

The figure below shows the basics of how the model works.  First, for some background regarding the lifecycle of the malaria parasite, see this wonderful diagram by the CDC.  In brief, the most virulent form of malaria is caused by an infection with the parasite Plasmodium falciparum.  This parasite is transmitted by the bite of an infected mosquito. The parasites enter through the puncture in the skin and travel to the liver, where they grow and multiply.  These parasites then emerge from the liver, where they travel to the bloodstream to infect red blood cells (RBCs).  These parasites are called asexual parasites, because they cannot reproduce.  The levels of asexual parasites rise very quickly (actually, geometrically), multiplying 8-20 fold every 48 hours.  The level of parasitemia continues to rise until checked by the body's immune systems, which eventually clear the infections over many days.

Some of these asexual parasites will go on to further develop into gametocytes, the sexual forms of the parasite.  If these gametocytes are taken up by a mosquito bite, they will then mate in the mosquito, form an oocyte and an oocyst, and prepare for emergence when the mosquito next bites a host (thus completing the cycle).

Our model simulates the blood stages of this cycle (the asexual and sexual stages), as well as treatment with an antimalarial drug.  The functioning of the model is illustrated in thefigure below.

In this figure, the model was run six times, assuming three individuals went untreated and three were treated with artemether-lumefantrine two days after first fever. Treated individuals are colored red/magenta/orange, untreated are blue/violet/green.

Panel A illustrates the log10 asexual parasitemias of the individuals over time. The inset depicts the first 50 days of infection; vertical bars indicate the day of first fever for each of the individuals. Triangles above indicate the first day of fever. The black line is the level of detectability by microscopy (10 PRBC/μL).

Panel B depicts the daily gametocytemias of the same 6 individuals. The gametocytemias are usually approximately 2 orders of magnitude less than the asexual parasitemias a few days prior. Treated individuals' asexual parasitemias and gametocytemias drop rapidly after treatment.

Panel C provides the estimated probability of human to mosquito transmission given the gametocytemias in B. The x-axis maximum is changed from 700 to 200; none of the 6 individuals were infectious after day 152. The areas under the infectivity curves are 3.3, 5.7, and 3.9 days for treated and 19.3, 25.7, and 23.0 days for untreated, respectively. Drug treatment with an ACT rapidly reduces the probability of onward infection. Although the model predicts the persistence of long-lived low-level and sub-detectable infections (as observed in malaria therapy), Panel C illustrates that these infections are usually not transmissive after the initial period of infection.

Fig 1

The fact that this model is able to reproduce the natural course of an infection, as well as the results of treatment, took some effort.  However, now that we have developed this tool, we are performing a variety of experiments with it, examining the effects of different treatments on sensitive and resistant parasites in silico.  We are also developing a standalone tool for use by researchers; however, we cannot share this tool as of yet.

The other projects that I am working on include a worldwide map of malaria endemicity (i.e. where malaria is most prevalent) as well as developing statistical tools for analysis of laboratory data using genetically-modified parasites.  Papers with results of these studies are forthcoming. 



Previous Publications:

“MPD Thruster Performance Analytic Models,” Gilland, J. and Johnston, G., AIP Conf. Proc. 654, 516 (2003), DOI:10.1063/1.1541334. Link to PDF


Links & Resources:

The Sustainable Development Doctoral Society sponsors a series of lectures throughout the year; you can find a syllabus here.


Forms:

Here is where you will eventually be able to enter comments, thoughts, etc., and post to the server.  But I just haven't had the time yet!  If you would like to contact me, please feel free to email and I will reply as soon as possible.




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