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Graduate Student Blog

by Mavra Nasir, Quantitative Biomedical Science (QBS)

Respiratory infections caused by Pseudomonas aeruginosa and Staphylococcus aureus are the leading cause of morbidity and mortality in cystic fibrosis (CF) patients(1). Accurate microbiological profiling of the lower airways and, consequently, prompt antibiotic treatment, are crucial for delaying chronic infections. In expectorating patients, sputum is cultured for detection of bacterial pathogens. Most children as well as individuals with mild CF disease do not spontaneously expectorate sputum(2,3). In non-expectorating patients, bronchoalveolar lavage (BAL) may be performed to diagnose lower airway infection. However, it is an invasive procedure that requires sedation and cannot be performed frequently. Hence, oropharyngeal (OP) swab cultures are used as surrogate specimens for species identification and antibiotic sensitivity determination. The existing literature is divided on the clinical utility of OP swabs as a reliable surrogate for BAL and sputum. Most studies on children report variable positive predictive values (PPV) ranging from 0.44 to 0.83 for P. aeruginosa and 0.33 to 0.64 for S. aureus(4-7).  In addition, current diagnostic techniques can take up to three days for pathogen identification.

Human breath consists of thousands of volatile molecules that result from cellular metabolic processes, environmental exposures, as well as contributions from the microbiome. Over the last decade, the Food and Drug Administration (FDA) has approved 13 breath tests for use in the clinic. Our work aims to identify putative volatile biomarkers in exhaled breath of CF patients, using two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS), that can guide pathogen identification and antibiotic treatment. Preliminary work involving ex-vivo BAL samples (n = 154) from CF patients were analyzed and a set of 11 volatile biomarkers was able to identify P. aeruginosa a sensitivity and specificity of 0.73 (95% CI 0.46-0.87) and 0.81 (95% CI 0.60-0.94) respectively in the validation set(8). The same set of biomarkers gave a sensitivity and specificity of 0.67 (95% CI 0.38-0.88) and 0.38 (95% CI 0.09-0.76) for S. aureus identification.

To demonstrate clinical translation, we are prospectively collecting breath and sputum from CF patients at CF centers in the United States (New Hampshire and Colorado) and Ireland. Preliminary results from breath show a higher sensitivity for P. aeruginosa and higher specificity for S. aureus compared to OP swabs, suggesting that biomarkers in breath can be used as screening tools to rule-in P. aeruginosa and rule-out S. aureus infections in CF patients.

REFERENCES

  1.        Rowe SM, Miller S, Sorscher EJ. Cystic fibrosis. N Engl J Med. 2005;352(19):1992-2001. doi: 10.1056/NEJMra043184. PubMed PMID: 15888700.
  2.        Radhakrishnan DK, Corey M, Dell SD. Realities of expectorated sputum collection in the pediatric cystic fibrosis clinic. Arch Pediatr Adolesc Med. 2007;161(6):603-6. doi: 10.1001/archpedi.161.6.603. PubMed PMID: 17548767.
  3.        Sagel SD, Kapsner R, Osberg I, Sontag MK, Accurso FJ. Airway inflammation in children with cystic fibrosis and healthy children assessed by sputum induction. Am J Respir Crit Care Med. 2001;164(8 Pt 1):1425-31. doi: 10.1164/ajrccm.164.8.2104075. PubMed PMID: 11704590.
  4.        Armstrong DS, Grimwood K, Carlin JB, Carzino R, Olinsky A, Phelan PD. Bronchoalveolar lavage or oropharyngeal cultures to identify lower respiratory pathogens in infants with cystic fibrosis. Pediatr Pulmonol. 1996;21(5):267-75. doi: 10.1002/(SICI)1099-0496(199605)21:5<267::AID-PPUL1>3.0.CO;2-K. PubMed PMID: 8726151.
  5.        Rosenfeld M, Emerson J, Accurso F, Armstrong D, Castile R, Grimwood K, Hiatt P, McCoy K, McNamara S, Ramsey B, Wagener J. Diagnostic accuracy of oropharyngeal cultures in infants and young children with cystic fibrosis. Pediatr Pulmonol. 1999;28(5):321-8. PubMed PMID: 10536062.
  6.        Ramsey B, Wentz K, Smith A, Richardson M, Williams-Warren J, Hedges D, Gibson R, Redding G, Lent K, Harris K. Predictive value of oropharyngeal cultures for identifying lower airway bacteria in cystic fibrosis patients. American Review of Respiratory Disease. 1991;144.
  7.        Jung A, Kleinau I, Schonian G, Bauernfeind A, Chen C, Griese M, Doring G, Gobel U, Wahn U, Paul K. Sequential genotyping of Pseudomonas aeruginosa from upper and lower airways of cystic fibrosis patients. Eur Respir J. 2002;20(6):1457-63. PubMed PMID: 12503704.

8.           Nasir M, Bean HD, Smolinska A, Rees CA, Zemanick ET, Hill JE. Volatile molecules from bronchoalveolar lavage fluid can 'rule-in' Pseudomonas aeruginosa and 'rule-out' Staphylococcus aureus infections in cystic fibrosis patients. Sci Rep. 2018;8(1):826. doi: 10.1038/s41598-017-18491-8. PubMed PMID: 29339749; PMCID: PMC5770459.

07/19/2018

by Mary Liza Hartong, Creative Writing **Winner of Best Overall Blog Post**

This month, I sent the first draft of my thesis to a friend. My precious, one hundred and thirty-three page thesis, my memoir, my heart and soul. She handed it back after a few days.

“I can’t believe Dartmouth is actually giving you a masters for writing stories about yourself.”

“You think this is easy?” I balked.

“Everything already happened,” she shrugged, as if I had photocopied twenty-four year’s worth of black and white composition notebooks and called it a day.

“Writing takes work,” I pushed.

“Eh,” she finished.

It was then that I remembered my friend studies physics. No disrespect to acceleration, gravity, and whatever the hell else those eggheads care about, but frankly, writing a memoir is pretty hard. First of all, there is the matter of remembering. As a child of divorce, there are plenty of stories I’ve buried that I never intended to be time capsules. I wanted them gone. Disintegrated. And here I am, shovel in hand, hoping they are right where I left them so that I can polish them up and make them worth something again.

This process has come with an unexpected perk: my sisters remember, too. Sometimes I’ll call and read them a story I’m working on and they’ll say, “Wait! Don’t forget what Mom said after that” or “No, we were detained for three hours, not two.” They hand me little nuggets of gold, details that lend the whole piece an extra sheen. And yet, some things they do not remember at all. Where I have a crisp memory of my mother kicking my father out, my oldest sister only remembers what we had for dinner that night. A small gesture can be lost in the dirt if I do not dig deep enough for it. As a writer, I have to constantly keep up the belief that my work is important. I suppose my physicist friend feels the same, that if she doesn’t complete the equations on time there will be hell to pay. We are, both of us, invested in the act of discovery.

So, perhaps I have fooled Dartmouth into granting me a masters for such frivolous work. Perhaps they have paid for a decadent foray into narcissism. But perhaps, like me, they know the value of memory, the value of digging, and the value of gold.

 

by Kimberley Lewis, MCB

**Winner of Most Informative Blog Post**

 

Impostor Syndrome, as defined, is the feeling of inadequacy or not belonging due to being under qualified for a particular position. As graduate students, most, if not all of us, have experienced this at least once. In fact, graduate students are high on the list of people who normally experience this phenomenon. The impostor feeling may last a few months, go away after a few days, or be just a fleeting thought. For me, the first time I felt it was during the process of preparing for my qualifying exam. I was inundated with dread at the thought of all I needed to learn to prepare for the defense, in addition to the looming deadlines. I realized very quickly that I had a decision to make: either freeze up and be overwhelmed or identify what the problem was and prioritize what I needed to accomplish. Since then, each time I have felt like an impostor I performed an internal assessment to identify the issues and tackled them one by one until all was back to rights.

What most graduate students fail to understand is that their qualifications have already been rigorously assessed during the application process for graduate school. Admission rates to graduate schools are usually very competitive, ranging from a 5-14% acceptance rate. Also, people who experience the Impostor Syndrome have been characterized as being high achievers, hard workers, and intelligent. Many famous people, for example Maya Angelou, who embody success, also have had the Impostor Experience.

With that being said, feeling this way occasionally should not be viewed as a weakness. Instead, it should be taken as a sign that maybe priorities need to be rearranged or that there might be a skill that can be strengthened in order to streamline our performance. As graduate students, we should spend our graduate career constantly performing internal evaluations in order to get the best out of graduate school in terms of growing as young professionals. Since feeling like an impostor is an indirect way of identifying our weaknesses or areas that need improving, we should aim to use this as an internal prompt for self-assessment. In doing so, we will be constantly aware of the things we need to work on in order to be well-rounded graduate students. So I say to my fellow comrades, let us turn the negativity associated with feeling like an impostor into positivity by focusing on improving ourselves. When you start to feel like an impostor, just remember that it too shall pass.

07 May 2018

by Aaron Karp **Winner of Best Research Writing blog post**

For my thesis I am investigating sonic spaces that exist under the coverage of mass surveillance technology. My aim is to identify the properties of sounds that make them “surveillable” and to create sounds that exist outside of surveillable spheres. There has been a moderate amount of investigation into issues of mass video surveillance from a theory standpoint, but surprisingly little research has been conducted within the realm of audio surveillance. What makes sound unique in the discussion of surveillance technology? Is there something about the listening that people view as less inherently sacred and private than seeing? With what we have learned from recent government whistleblowers and the state-of-the-art technological capabilities of surveillance systems, it is clear that all citizens in Western society should operate on the assumption that they are always being listened to. Given this reality, the need for a technology that responds to such an invasion of privacy is apparent.

 

Surveillance technology at its core attempts to identify “important” versus “unimportant sounds” and categorize them into further degrees of utility. An example of a technology I’m referring to is speech transcription software. A speech detection system would first perform what is known as a source separation task, where it would attempt to separate out spoken words from background noise in a recording that contains both sounds on top of each other. After this point the algorithm would try to understand what words were being said and then flag words and phrases of significance. These algorithms work because of physical properties of speech (the “important” sound) in comparison to something like a washing machine whirring (the “unimportant” sound). In other words, the speech often looks different to the machine on a fundamental level. In the early days of Machine Listening these differences were explored as mathematical truths, but the properties of those maths can only extend so far. Presently most source separation algorithms are employing some level of machine learning, and the most cutting-edge research revolves around deep learning techniques using massive amounts of data.

My project attempts to understand why some sounds are easily separated and others are not. I will then be creating a system to synthesize sounds that, when played in conjunction with “important” sounds, result in sounds that don’t have the properties that would identify them as “important”. This process would convert “important” sounds to “unimportant” ones, marking them as useless and thus makes them, for all intents and purposes, undetectable.

04 May 2018

 

Greetings! We would like to take a moment and say thank you to everyone who submitted a blog post for our competition during GRAD Appreciation Week. We got over 15 submissions from almost every Department/ Program on campus, which is great turnout for graduate students! We hope that everyone stays tuned in the next few weeks as we publish the posts that were submitted. Tomorrow you'll get to read the first, which was awarded "Best Research" writing in the competition. Want to know who won and what they wrote about? See below for all the winners! Be sure to continue submitting blog posts to share your opinions about Dartmouth research/ life.

Also, a big congratulations to the Digital Musics program for the highest participation level thereby winning them a party for the program! 

Honorable Mentions:

Sadie Doran [Thayer School of Engineering]: Sadie wrote a letter to Dartmouth proclaiming her love from the moment she set foot on campus.

Mavra Nasir [Quantitative Biomedical Sciences]: Mavra submitted a post describing her research as well as a quirky field guide to being a graduate student.

Kyle Morrison [Molecular and Cellular Biology]: Kyle wrote honestly about the emotional toll of graduate school.

Camilla Tassi [Digital Music]: Camilla wrote about her research into the modern performance of early works of music.

Hannah Grover [Thayer School of Engineering]: Hannah wrote about what it's like to be in Thayer and what her day looks like.

Award Winners:

Most Informative: Kimberley Lewis for “Impost Syndrome: Internal Prompt” [Molecular and Cellular Biology]: Kimberley wrote about why we feel like we aren't good enough, but that in the end, this too shall pass.

Most Interesting: Dominic Coles for “Leave the Needle on the Jammed Wavelength” [Digital Music]: Dominic explained his research into the role of jamming radio signals in impeding the independence of colonized nations.

Most Honest: Hyun Seong [Computer Science]: Hyun spoke about what graduate school can do to you and how it can be a weary road.

Best Research Writing: Aaron Karp [Digital Music]: Aaron explained his work into massive audio surveillance systems that must decipher important vs unimportant sounds to extract the relevant information.

Best Overall: Mary Liza Hartong [Creative Writing]: Mary Liza explained that even though her thesis is a memoir, it is just as difficult as any other degree - including physics!

If you would like to be involved in the GRAD Blog don't hesitate to reach out with any questions! You can get in touch by clicking here.

 

'Til next time,

Savannah Barnett

by Samantha Sobol

January 29, 2018

Panel members of post-doctoral and graduate student women speaking on issues women face in the sciences. PC: Samantha Sobol

The Women in Science Post-doctoral and Graduate Student Panel event was a safe space for the Dartmouth community to discuss effective ways to navigate sexism that is pervasive, especially in the STEM professional world. Individuals on the panel shared their personal experiences with how they have been able to triumph over gender discrimination as a woman in academia and in STEM. The event also included dinner where GWISE students and the overall graduate community could interact. Even as a student affiliated with MALS, I found this event to be incredibly inspiring and useful. This is the type of event that creates an open dialogue so change can be effectuated against gender inequality.

A group of attendees and volunteers participating in the game after the panel to workshop skills to have in the sciences. PC: Samantha Sobol

The workshop was an effective way to think about what is most critical to have a good workplace environment. Smaller groups were formed to talk about what issues we individually think are necessary for a positive workplace. A few ideas were selected from each group and then we debated in a larger discussion, weighing the pros and cons of each concept. Some of these ideas included having consistent research results and open-mindedness. The debate exercise was a valuable way to practice conveying our ideas verbally on the spot. As a collective group we voted on two issues discussed that were most important to us. We unanimously said that there is no place for sexism of any kind within any environment, in particular a professional one and that working overtime shouldn’t be a constant in a person’s schedule.

 

by Samantha Sobol

January 22, 2018

Graduate students making vision boards for the new year and beyond. Photo: Samantha Sobol

To start off the new year, Graduate Student Activities Coordinator, Sara Perz-Hintz, organized a gathering of students to create a visual representation of where they want to be in the next year. The overall tone of the event was friendly and it was a great way to meet other grad students! It was cool to see how everyone's vision board was a unique representation of themselves. The light-hearted crafting environment made it a comfortable place to delve into self-development. The worksheets were a very helpful way to plan for the upcoming year and even included goal-setting for five and ten years from now. I didn't expect to think about how my life might be a decade from now. Thinking about plans from a bigger-picture perspective was beneficial for me. 

See if you can make a vision board on your own and include goals for the future. We don't get much time to think about what we will do after graduate school. But take 10 minutes this weekend and ask yourself where you want to go, what you want to do, who you want to be near after graduation. Then start setting smaller short-term goals to make those things happen. Does anyone know of a resource to help with this kind of planning? Comment on this post to start a conversation and share resources!

The proposed House GOP tax plan is detrimental to graduate education.

Under the proposed tax plan tuition waivers are to be considered taxable income. Dartmouth tuition will be considered as earned income, increasing your taxable income by ~$50,000/year (Dartmouth 2017-18 Schedule of Charges). Although your stipend would remain the same, you will be in an increased tax bracket, paying taxes on your tuition and stipend as though they were both earned income! Please see below for more information and what you can do about it.

We are calling on all graduate students to contact your representatives!