Seminars

Upcoming Seminars / Seminars This Week



Mon 12/9/13 11 am	Volen 201
Computational/Systems Neuroscience Journal Club
Nancy Kopell (Boston University)
Cortical Rhythms Facilitate Bottom-Up and Top-Down Processing
Ref: Top-down beta rhythms support selective attention via interlaminar interaction: a model. Lee JH, Whittington MA, Kopell NJ. PLoS Comput Biol. 2013 Aug;9(8):e1003164; Dual gamma rhythm generators control interlaminar synchrony in auditory cortex; Ainsworth M, Lee S, Cunningham MO, Roopun AK, Traub RD, Kopell NJ, Whittington MA. J Neurosci. 2011 Nov 23;31(47):17040-51.
Brain rhythms are known to be associated with many aspects of cognition and can be produced in many physiological ways. But it is not understood how or even if the physiology of brain rhythms can support the cognitive correlates associated with these dynamics. The talk focuses on the physiology of the rhythms and discusses several examples showing how brain rhythms can dynamically regulate the flow of electrical signals within a cortical column and between regions.
Hosted by Keith Hengen
Mon 12/9/13 12 noon	Rosenstiel 118
Molecular Genetics Journal Club
Joanne Kamens
Professional Development Seminar
Abstract: We all hear the buzzword of "mentoring" in relation to career success but most of us don't know how to look for a strong mentor or how to use once effectively once we have found one. These presentations give practical advice about finding, utilizing and being a mentor in a fun, interactive format. Speaker Bio: Joanne received her PhD in Genetics from Harvard University, where she studied signaling pathways. She spent 15 years in the pharmaceutical industry at Abbott Research Center and moved into the biotechnology sector as Senior Director of Research Collaborations at RXi Pharmaceuticals. Joanne also has extensive experience with leadership of non-profit organizations. She founded the Massachusetts chapter of the Association for Women in Science (AWIS) and is Director of Mentoring for the Boston chapter of the Healthcare BusinesswomenÕs Association (HBA),
Hosted by Genetics Training Grant
Mon 12/9/13 4 pm	Gerstenzang 121
Chemistry Department Colloquium
Joseph Sadighi (Georgia Institute of Technology)
Small Clusters of Group 11 Metals Supported by N-Heterocyclic Carbenes
Hosted by Casey Wade
Tue 12/10/13 12:30 pm	Gerstenzang 121
Neurobiology Journal Club
Marjena Popovic (Van Hooser lab)
A functional and perceptual signature of the second visual area in primates
Ref: Freeman, Ziemba, Heeger, Simoncelli, Movshon, Nature Neuroscience 2013
Sonal Shruti (Marder lab)
Social reward requires coordinated activity of nucleus accumbens oxytocin and serotonin
Ref: Dolen G, Darvishzadeh A, Huang KW, Malenka RC. Nature, 12 September 2013, Volume 501 (Pages 179-184).
Wed 12/11/13 9:30 am	Volen 201
Thesis Seminar (Graduate Program in Psychology)
Abigail Noyce (Sekuler Lab)
Neural processes for learning and monitoring sequential regularities in changeable environments
The world is largely stable and predictable. Humans and other organisms are sensitive to that stability, and use it to support cognitive processes. This work consists of a series of studies that explore how humans learn about such stability, use that information to generate predictions about forthcoming sensory input, and detect when such predictions are inadequate. First, I present a modeling study that quantified the distributions of errors that people make on a complex, visuomotor sequence learning task, and examine the serial position dynamics of several parameters describing short-term visual memory. Both precision and capacity for these sequences increases with familiarity, and the worst-represented items show the largest increases. Next, I present an experiment that used the same task to understand the effects of deviant items within familiar sequences. By measuring ERPs to new, familiar, and deviant items, I dissociate the neural activity associated with detecting a deviant from that associated with encoding task-relevant stimulus characteristics. Finally, I present an experiment investigating the role of prediction in a task that is stochastic, rather than sequential, and in which deviant events occurred among the distractors rather than among the task-relevant stimuli. Unexpected events among the distractors seem to obligatorily attract attention, enhancing or impairing performance. Further, I show that the individual differences in the neural response to such unexpected events is predicted by temperament. Together, these studies illuminate how the brain learns about predictability in a range of settings, and leverages such predictability to facilitate cognition.
Wed 12/11/13 2 pm	Abelson 229
Special Seminar
SCOPE student presenters (Olin College of Engineering)
Collaborative Senior Capstone Project (SCOPE) with Olin College of Engineering Mid-Year Update: Rapid Prototyping of Microfluidic Foil Chips
Microfluidics is a rapidly growing field that has gained popularity over the past decade in a wide range of applications. Despite the popularity the field has gained, limitations still exist as the technology remains mostly in the academics.1 The goal of the Olin-Brandeis 2013-2014 senior capstone project is to investigate rapid prototyping of microfluidic foil chips to work towards creating an ecosystem for prototyping with new materials at new speeds with possible commercial applications. To do this, the team is working to optimize a thermal linear press to successfully hot-emboss 50 m wide by 50 m tall channels in cyclic olefin co-polymer (COC). The team will also work to deliver a prototype of a rolling hot embosser for future embossing experimentation with stainless steel masters at Brandeis University.   Works Cited [1] Whitesides, George M. "The Origins and the Future of Microfluidics." Nature 442.7100 (2006): 369--373.
Hosted by Dongshin Kim
Thu 12/12/13 12 noon	Volen 101
Language Technology Seminar Series
Annie Zaenen (Stanford University)
When you aren't Stupid, you don't do Stupid Things: Implicative Uses of Evaluative Factive Adjectives
Ref: Before retiring in 2010, Annie Zaenen was a Principal Scientist in the Natural Language Theory and Technology group at PARC. She is now a consulting professor in the Stanford Linguistics Department and a Senior Researcher at CSLI.
Evaluative adjectives such as stupid, smart, lucky, sweet, and cruel can take propositional complements as in (1):  1. John was smart to leave early. In this construction they are generally considered to be factive, i.e.: 2. John was not smart to leave early. is supposed to mean that John did leave early and that it was not a good idea. When one looks at the web, however, one finds easily examples where the intended meaning is not factive, as in the following: 3. Luckily, I was not stupid to send them any money. Amazon Mechanical Turk experiments and corpus studies confirm the existence of this pattern. We will discuss whether it should be seen as a performance error or whether there seems to be a real 'dialect' split among speakers of (American) English. Whatever the analysis, it seems that the pattern is prevalent enough for NLP applications that assign factuality judgments to events to need to take such variations into account.
Lunch will be served
Hosted by James Pustejovsky
Thu 12/12/13 1 pm	Abelson 131
Thesis Seminar (Graduate Program in Molecular and Cell Biology)
Yue Li (Rosbash Lab)
The role of the period protein in Drosophila circadian rhythm: Exploring the effects of the original perS and perL mutations
Thu 12/12/13 2 pm	Gerstenzang 121
Thesis Seminar (Graduate Program in Chemistry)
Yongwei Wu (Deng Lab)
Biomimetic Proton Transfer Catalysis with Organic Molecules
Thu 12/12/13 3 pm	Shapiro Science Center GL14
Special Seminar
Alexis Gatreau (CNRS, France)
Hosted by Bruce Goode
Thu 12/12/13 4 pm	Abelson 229
MRSEC Seminar
Jason Perlmutter (Brandeis University)
Simulations of Capsid Assembly around Polyelectrolytes or Nucleic Acids
For many viruses, the spontaneous assembly of a capsid shell around the nucleic acid (NA) genome is an essential step in the viral life cycle. Understanding how assembly depends on the structure of the capsid proteins and the NA could promote biomedical efforts to block viral propagation and guide the reengineering of capsids for gene therapy applications. We present a coarse-grained model of capsid proteins and NAs with which we investigate assembly dynamics and thermodynamics. In contrast to recent theoretical models, we find that capsids spontaneously Ôovercharge'; that is, the NA length which is kinetically and thermodynamically optimal possesses a negative charge greater than the positive charge of the capsid. When applied to specific virus capsids, the calculated optimal NA lengths closely correspond to the natural viral genome lengths. Simulations using linear polyelectrolytes rather than base-paired NAs result in optimal lengths shorter than the viral genomes, demonstrating the importance of NA structure to capsid assembly. These results suggest that the features included in this model (i.e. electrostatics, excluded volume, and NA tertiary structure) are sufficient to predict assembly thermodynamics and that the ability of viruses to selectively encapsidate their genomic NAs can be explained, at least in part, on a thermodynamic basis.
Hosted by M. Hagan
Fri 12/13/13 10 am	Rosenstiel 118
Thesis Seminar (Graduate Program in Molecular and Cell Biology)
Alexander Ferrazzoli (Lovett Lab)
Regulation of the Escherichia coli DNA damage response by IraD, an alternative sigma factor stabilizer
Fri 12/13/13 11:15 am	Gerstenzang 121
Biochemistry-Biophysics Friday Lunchtime Pizza Talks
Adrian Whitty (Boston University)
Small Molecule Inhibitors of Protein-Protein Interactions
Hosted by Liz Hedstrom
Fri 12/13/13 12 noon	Volen 101
Language Technology Seminar Series
Martha Palmer (University of Colorado, Boulder)
Beyond Shallow Semantics
Abstract: Shallow semantic analyzers, such as semantic role labelers and sense taggers, are increasing in accuracy and are becoming commonplace. However, they only provide limited and local representations of words and individual predicate-argument structures. This talk will address some of the current opportunities and challenges in producing deeper, richer representations of coherent eventualities. Available resources, such as VerbNet, that can assist in this process will also be discussed, as well as some of their limitations. The talk will end with some Abstract Meaning Representation (AMR) examples. Speaker Bio: Martha Palmer is a Full Professor at the University of Colorado with joint appointments in Linguistics and Computer Science and is an Institute of Cognitive Science Faculty Fellow. She recently won a Boulder Faculty Assembly 2010 Research Award. Her research has been focused on trying to capture elements of the meanings of words that can comprise automatic representations of complex sentences and documents. Supervised machine learning techniques rely on vast amounts of annotated training data so she and her students are engaged in providing data with word sense tags and semantic role labels for English, Chinese, Arabic, Hindi, and Urdu, funded by DARPA and NSF. They also train automatic sense taggers and semantic role labelers, and extract bilingual lexicons from parallel corpora. A more recent focus is the application of these methods to biomedical journal articles and clinical notes, funded by NIH. She is a co-editor for the Journal of Natural Language Engineering and for LiLT, Linguistic Issues in Language Technology, and on the CLJ Editorial Board. She is a past President of the Association for Computational Linguistics, past Chair of SIGLEX and SIGHAN, and was the Director of the 2011 Linguistics Institute held in Boulder, Colorado.
Lunch will be served
Hosted by James Pustejovsky
Fri 12/13/13 12:30 pm	Shapiro Science Center 1-03 Library
Fly Fest
Orie Shafer (U. Michigan)
Connectivity Hierarchy and Coupling in a Circadian Clock Neuron Network
Hosted by Rosbash Lab
Fri 12/20/13	Gerstenzang 121
Biochemistry-Biophysics Friday Lunchtime Pizza Talks
TBA (TBA)
Fri 1/3/14 11:15 am	Gerstenzang 121
Biochemistry-Biophysics Friday Lunchtime Pizza Talks
1st yr grads
Rotation Talks
Thu 1/9/14 8:45 am	TBA
Quantitative Biology Program
TBA (Annual Quantitative Biology Bootcamp)
Fri 1/10/14 12:30 pm	Gerstenzang 123
Molecular and Cell Biology & Neuroscience Student Seminars
Marjena Popovic (Van Hooser Lab)
Katelyn Kenny (Paradis Lab)