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Graduate Student Blog

by Xanthe Kraft **Blog Competition**

10/08/2018

 

As someone who did her undergrad at Dartmouth, people ask me if I’m “sick of Hanover” or tired of Dartmouth, as I approach the 6-year-mark. Because I’ve changed my focus from Earth Science to Computer Science, then Philosophy, Digital Arts and now Music Composition, I could hardly tire of anything save the library KAF line. But even so, I recognize something special about being a graduate student that my undergraduate education lacked, that transforms the way I experience the same resources and place— Integrity, or ‘wholeness’, in an old way of understanding the word. Now, as a Master’s student in Digital Musics, my whole life encircles one focus, one meditation, one ever-growing framework on understanding Beauty, Art, and its interactions and implications in our technology-laden world.

 

I tell people I love grad school SO much more than undergrad, not because I didn’t love my A cappella group (which, honestly became a higher priority than my classes themselves), or partially enjoy those dramatic study buddy woes and all-nighters that defined “working hard” in that environment (an odd type of “hard-work signaling”, if you will), or taking spontaneous runs into the woods because I can (and because I’m some medieval fairy artist). But because now I live an extremely monotonous, cyclical, balanced, sole-purposed life. And I love it.

 

I have a regular sleep schedule, whereas I previously scraped the sanity of the wee hours for those juicy late-night thoughts and tunes that mostly aren’t that good, I just think they are because I’m tired. I work-out regularly, cook and make my own nutritious food (balancing good for the body with good for the soul), and *usually* stop researching at a reasonable evening hour. I get artistic inspiration between 9am and 12pm, writing like a madwoman until my alarm interjects, and then I flip to analyzing my Seminar’s readings for the week, or practicing voice. In the quiet moments from event to event, I casually sift my studies through mundane tasks, yielding surprising fruits. On evenings and weekends, with my grad school buddies, our jokes require a shared mastery of material, and we reap our common subjects for all their numerous humorous rewards. Yet, these reoccurring, regimented events all contribute to the singularly focused and free contemplation of my work.

 

Living such an integrated life enables me to somehow always further my academic goals, even when I’m doing something seemingly unrelated or taking a break altogether. By constraining myself with my schedule, and not being divided by so many superfluous tasks and decisions, I’m free to dedicate myself wholly to my work, and pursue it to highest degree possible, for me right now (I am, after all, only a Master’s student). While I still have many spontaneous moments, as one must, my life looks less interesting, but is more. I love what I do, I love what I study, and I love doing what makes that work. I can’t help but think this is always how school’s supposed to be.

 

by Mavra Nasir and Ted Mellors **Blog Competition**

09/20/2018

 

The authors would like to acknowledge that there is a conflict on the order of author list. Neither party wants to take credit for this piece of work.

Nasir: Andy Dufresne had to crawl through five-hundred yards of sewer pipe in order to escape from Shawshank prison. Finishing up my fourth year of graduate school, I think I might be stuck halfway through that pipe.

I came to graduate school because I love asking questions. No amount of chocolate in the world could silence the “why’s?” that rolled off my tongue faster than one can imagine, and believe me, my parents tried. I can’t recall what I was expecting graduate school to be like, but it certainly wasn’t this. I have learnt a few things along the way, so I wanted to provide a survival guide for the brave unfortunate souls considering this feat:

  1.   Not all PhD’s are created equal. Accept it.
  2.   You may think your insight is always appreciated. It really isn’t. Try changing the tone.
  3.   Nobody is trying to steal your ideas. Period.
  4.   If you are running experiments 24/7, you are doing something wrong.
  5.   Listen to your mentor.

At this point, you are probably expecting me to make a cheesy hopeful remark. What I do know, is that if you stick with it, you are going to learn a lot. That is one thing I cannot dispute. Graduate school has been hard, but the beauty of a ‘you-just-left-me-speechless’ question, and a simple experiment as an answer, might just be worth it all. After all, Andy Dufresne did get out.

Mellors: You can’t. *Bottoms-up*

by Dominic Coles **Blog Competition**

9/8/2018

 

Across the colonized world, people resisting the oppressive forces of imperialism placed their ears against the radio receiver, attempting to decipher its noisy signal, jammed by the interference of the colonizers. In that noise was a voice obscured; they imagined its words. It spoke of independence, of fierce protests and battles; it sang national songs and anthems. These listenings would provide a tactic which would become central to the creation of a post-colonial collective politics. Listening was a means of organizing and reclaiming a collective narrative, a history, present, and future; noise was the site in which this tactic of listening could be practiced.

Frantz Fanon detailed this larger historical trend as it specifically unfolded during the Algerian War of Independence in his essay, “This Is the Voice of Algeria.” The radio was initially introduced into the colonial landscape as a means of disseminating colonial ideals, culture, and propaganda. With unchecked control of the information disseminated on Radio-Alger, the national broadcasting service, the French hoped to bolster the authority of their colonial powers in Algeria. Broadly rejected by native Algerians, the device was first taken up by French expatriates living abroad in Algeria.

A decisive shift occurred in Algeria’s relationship with the radio in 1951, coinciding with the onset of skirmishes in Tunisia. With an increase in revolutionary activity, Algerians felt the need for an expanded news network consisting of non-French sources. Shortly thereafter, the show Voice of Free Algeria was established, its sole purpose to broadcast radical, revolutionary news each day. The traditional familial resistances to the radio broke down in light of the need for information and gradually the radio was stripped of its ties to French cultural oppression. Of primary interest to my research is the phenomenon that Fanon documents next. He details the French practice of sound-wave warfare in which the broadcasting wavelengths of the Voice of Algeria would be detected and systematically jammed so that the broadcasts themselves were rendered noise. Listeners would remain, with a single interpreter, ear fixed to the radio, tuning the dial in the hopes of finding the Voice, now broadcast on a new frequency, but only to be jammed again. The interpreter would relay fragments of the broadcasts to those gathered and listening, but they were largely indecipherable. This was not a hindrance: instead, gathered listeners would imagine the Voices words, transplanting their individual interpretations, hopes, dreams, and visions of utopia to the scattered noise of the broadcast. As Fanon goes on to detail this phenomenon, it becomes increasingly clear that the Algerian listeners do not need to be able to decipher the Voice, rather, they gather daily to sit and listen to the radio’s noise, to the static produced by the jammed signals. My current research seeks to trace this same practice of listening and engaging with noise as a revolutionary tactic against colonialism through archival research and interviews with family members in India who lived through their own Independence movement.

by Matteo Visconti Di Oleggio Castello

05 September 2018

 

Twitter post by Matteo about the conference and a Twitter shoutout about his presentation from an audience member.

This past June I presented our work “ReproIn: automatic generation of shareable, version-controlled BIDS datasets from MR scanners” at the Organization for Human Brain Mapping meeting in Singapore. In recent years, the international neuroimaging community pushed forward initiatives to create standard data formats to enhance reproducibility and transparency, with the goal of increasing sharing of datasets across researchers. Adoption of an open and common standard also allowed the creation of analysis routines that can be tested and shared across centers, increasing the reliability of research in Cognitive Neuroscience.

At the Dartmouth Brain Imaging Center (http://dbic.dartmouth.edu/) we developed an automated pipeline to standardize Magnetic Resonance (MR) datasets into the Brain Imaging Data Structure (BIDS) format directly from acquisition. In the past, researchers had to manually convert these datasets—a painstaking task that took away much of precious time needed to address important scientific questions. With our pipeline, PIs and graduate students in our center can start using automated open tools the same day they collect their data. In the spirit of open science, we released all our material freely (http://reproin.repronim.org), so that other researchers around the world can also save time and improve their data curation practices.

I presented this work at the Informatics oral session during OHBM. The talk was very well received and a large audience attended, comprising international leaders in the field and young investigators. The large attendance showed the importance and need for such automated tools by the neuroimaging community. Because our work is based on open tools, my talk also highlighted the importance of contributing to open source software to avoid “reinventing the wheel” and provide the community with stable and reliable means to advance the science in our field. After the talk and during the poster presentation, I had many insightful discussions that will guide the future development of our pipeline.

I was able to present in Singapore thanks to the support of the Graduate Student Council, the Neukom Institute, the Department of Psychological & Brain Sciences, and my advisor, professor M. Ida Gobbini. This work was co-authored by researchers from three different institutions, to whom I’m deeply grateful for their help. At Dartmouth, James Dobson, Terry Sackett, Chandana Kodiweera, James Haxby, and Yaroslav Halchenko; at MIT, Mathias Goncalves and Satrajit Ghosh; and at the University of Magdeburg, Germany, Michael Hanke. Support for the development also came from grants NIH #1P41EB019936-01A1, NSF #1429999. Slides from my talk are available here and a copy of my poster can be found here.

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