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Graduate Student Blog

by Kayla Duval **Blog Competition**

12/08/2018

 

Transitioning from the bustling city of Boston to the sleepy small town of Hanover as a twenty-something year old was definitely a shock to the system. Gone were the days of endless food options, bar hopping through the city till 2am, and public transportation at night/on the weekends. These were replaced with debates on whether we should go to Thai Orchid or Tuk Tuk, drinking our way through the three rooms at the Hop and being asleep by 1215am, and committing to walking home after a night out. For many, NH small town life is like a whole different world – from the weather extremes, to the minimal indoor activities (RIP Shenanigans). Even for me, a born and raised New Hampshirite, Hanover was a whole new level of small town life. It’s easy to fixate on the remoteness of Hanover, but in actuality Hanover is a great place for grad school. Being at Thayer is like being back in high school; there’s only 100 PhDs so you know everyone, and of that 100 you really know 50% and you really really know 20-30%. In the 2.5 years I have been here, I have tried so many new things, become way more outdoorsy, and had way more fun than I ever thought possible, thanks to Thayer grads I really really know; it’s like its own little (big) family of friends. We have gone to countless DOC cabins, in the dead of summer and the dead of winter, cooking giant meals, and singing an eclectic range of songs around the fire. We have gone to Maine and canoed along the Saco river, camping along the edge and somehow not getting lost. We have hiked countless mountains from Moosilauke to Washington, with groups ranging from 5 people to 25 people. Winter is a time that many people struggle with because of the cold and snow, but I and others have recently learned how to ski so we can now join our friends and have ski trips with 20 of us at varying ski levels all having a blast. We have an annual Friendsgiving that grew to almost 50 of our closest friends this year and was a great time. We have random movie nights taking advantage of the giant screens in Thayer, and impromptu trips to cities like Nashville. On any given Thursday you can find anywhere from 5 to 20+ of us at Ramuntos, and at other times at Canoe. Outside of the social events, you can also overhear us talking about the wide range of research topics we each work on. I now know more about robots in Antarctica, buoys in Greenland, space weather, using bioimpendance to develop new surgical devices, circulating tumor cells for cancer diagnostics, and protein design than I ever would have thought possible. I guess what I am trying to say is that Thayer is an amazing place full of hard work on super cool research, and totally rad people who love to have fun outside of work.

by Christopher Helali **GSC Travel Grant Recipient**

11/20/2018

 

I would like to thank the Graduate Student Council for awarding me the Conference Travel Grant which gave me the opportunity to attend the 24th World Congress of Philosophy in Beijing, China. This conference, which occurs once every five years, was hosted by Peking University and had approximately 8,000 registered participants. I was able to present my research to distinguished scholars and students from around the world. In my paper entitled, “The Ancient of Days: Semiotic Multivalence and Oikonomia in Byzantine Iconography,” I spoke about my ongoing research on icons, some of which has been conducted at the Museum of Russian Icons in Clinton, MA. The panel I was presenting in was on Byzantine Philosophy with most of the participants being Chinese scholars of Byzantine philosophy and theology. Their questions were phenomenal and delved into a wide field of philosophical inquiry, bringing up theories and insights from early Christian theologians all the way to Derrida and contemporary anthropologists of modern Greece. During the conference, I had the opportunity to hear Judith Butler give the first ever Simone de Beauvoir endowed lecture at the congress on the topic of gender, language and translation, as well as to listen to Peter Singer from Princeton University speak about animal ethics and rights. For me, the highlight of the conference was seeing my former philosophy professor, close friend and comrade Rodney Peffer along with my comrade and friend Thalia Fung from the University of Havana who both presented on roundtables together on topics ranging from contemporary developments in Socialism, feminism, and the rise of the alt-right. This congress, attended historically by philosophers like Nobel laureate Bertrand Russell, is an opportunity to build internationalism and solidarity amongst people's not only from the core of the world-system, but from the Global South, whose voices are rarely heard. It was a great honor and privilege to have attended this conference and I am thankful for the Graduate Student Council for helping to make this a reality.

by Baihao Shao **GSC Professional Development Support Fund**

11/08/2018

 

With the generous support from Graduate Student Council, I was able to attend the influential workshop titled as “Molecular Rotors, Motors and Switches” in Telluride, Colorado at June of 2018. Leading scientists in our field, including 2016 Nobel laureate in Chemistry (Prof. Sir Fraser J. Stoddart), were invited to the workshop and gave interesting and inspiring presentations during that week. The telluride workshop is known for its condensed size with about sixty participants (including forty professors, and twenty postdocs and graduate students). Ample time was given to have deep discussions in science and establish collaborations.

            I was giving a poster presentation on the first day of the workshop, where I shared recent advances I have achieved in hydrazone-based photochromic molecules in our laboratory with colleagues. During that three hours, I have answered questions raised by my colleagues, who are interested in utilizing our molecules to build up new molecular machines. Meanwhile, I also received rewarding comments and opinions on my current research project and, had insightful discussions that helped to tackle a few problems I carried to the workshop. In addition, I stopped by others’ posters, including the beautiful works we used to discuss in weekly journal club at Chemistry Department, and had very beneficial talks with those researchers.  

            Within that week, about thirty invited speakers, including my advisor Prof. Aprahamian, were presenting the most recent research done in their research groups. Among them, the talk given by Prof. Nobuyuki Tamaoki from Hokkaido University (Japan) left deepest impression on me. His strategy of developing a photoswitchable ATP (AzoTP) to control the biological motor (kinesin) was very impressive. In the video he showed, the visible microtubes driven by kinesin were traveling with UV light, as the AzoTP can be activated with exposure to UV irradiation.  Inspired by his work, I think that interfacing the chemistry with biology in our lab will also deliver interesting research using our photoswitchable hydrazones.

            The most important thing in attending this workshop is that I am able to talk with all the attended professors and young scientists. During the rest periods, I could approach presenters and have further communications on their talks, and also conduct face-to-face conversations with “authors” on confusions and questions generated when reading their publications. In all cases, the professors and young scientist were quite open to discussions and willing to give information as plenty as possible. I was always able to receive more detailed and persuasive explanations on those scientific questions.

            As a second-year graduate student, I really benefit a lot from an experience of participating into a workshop like this. I got a better understanding on the field I worked in and, built up more confidence on carrying out my own research. Not only that, I have better ideas on how the scientific community works and what kind of requirements should be fulfilled in order to be a qualified scientist. In the end, I want to thank Graduate Student Council again for funding me to attend this fantastic workshop!  

 

by Camilla Tassi **Blog Competition**

10/20/2018

 

In my background as an early music singer and computer scientist, I find myself asking questions regarding performance of early repertoire in the contemporary age. Carissimi’s Jepthe was first performed in 1648 at the S.S. Crocifisso oratory in Rome. Its audience was surrounded by the architectural and visual elements/frescos of the venue, which are missing from today’s concert performances. At present, we are hundreds of years, and miles, away from the composer’s intended location of the piece’s performance, we do not speak the language of the work, and we may not come from its cultural and religious environment. The music speaks to us, but we lack a layer of accessibility to the composition that can help us understand it at a fuller, more complete, level. This role provides the chance for design and movement to evoke the missing layers.

 

In designing the projections for this work, I took a musical grounding: each prevalent musical key area is represented by a color. For example, blue is for G major, red for F major (often associated with Jepthe), A minor as white (a key introduced during the most tragic portion of the story’s prophecy), and so on. On the other hand, for the more representational imagery, the inspiration came from the text and narrative. This is seen in the battle of Ammon, which includes an image depicted by 17th-century baroque painter Nicolas Poussin, who spent most of his life working in Rome. At times, the musical writing’s density was of interest: the single vertical line for the narrator’s voice is contrasted by a large number of intersecting lines relating to the SATB texture during the first full chorus “Transivit ergo Jepthe”.

Language is wedded to the music. As a result, translations are incorporated as part of the set, not as separate elements. I was interested in avoiding program note translations or supertitles, which are located away from the performers, in order to instead keep language as part of the central narrative action.

The relationship across mediums (audio and visual) is one that continues to raise questions and provide various interpretations. Dartmouth’s campus and collaborations across art forms provides the platform for experimentation in performance. Projection is similar in properties to light in movement, color, intensity and distribution—all areas that one comes across in this production, particularly in transitions and animated imagery. In this work, the staging and projections work in conjunction to bring the dramatic narrative and music of Jepthe to a secular performance space—all in the spirit of the baroque period’s spectacle and history.

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.