Brandeis Receives Major Grant from the Mellon Foundation

Brandeis University has received a major grant to expand the LAPPS Grid Project that seamlessly connects open-source computer programs to quickly analyze huge amounts of language from diverse sources and genres.

James Pustejovsky

James Pustejovsky

Brandeis University has been awarded a two-year, $390,000 grant from the Andrew W. Mellon Foundation to lead an international collaboration to link the two major American and European infrastructures for the computational analysis of natural language. The resulting meta-framework has the potential to transform scholarship and development across multiple disciplines in the sciences, language and social sciences, and digital humanities by enabling scholars in Europe, the US, and Asia to work seamlessly across a massive range of software tools and data resources, developed separately by the American and European efforts. Led by James Pustejovsky, the TJX/ Feldberg Professor of Computer Science at Brandeis, the project team includes Nancy Ide (Vassar College), Erhard Hinrichs (University of Tübingen), and Jan Hajic (Charles University Prague).

The Language Applications (LAPPS) Grid Project—a collaborative, NSF-funded effort among Vassar, Brandeis, Carnegie Mellon University, and the Linguistic Data Consortium at the University of Pennsylvania—and the European Common Language Resources and Technology Infrastructure (CLARIN) are both frameworks (“grids”) that create and provide access to a broad range of computational resources for analyzing vast bodies of natural language data: digital language data collections, digital tools to work with them, and expertise for researchers to use them. Within each framework, members adhere to common standards and protocols, so that tools and data from different projects are “interoperable”: users can access, combine, and chain data from different repositories and tools from different sources to perform complex operations on a single platform with a single sign-on.

But the LAPPS Grid and CLARIN are not themselves interoperable. Researchers using data and tools in one framework cannot easily access or add data and tools from the other. LAPPS Grid users cannot access CLARIN’s multi-lingual services for digital humanities, social sciences, and language technology research and development, like Prague’s tools for search of oral history archives (developed to support their hosting the USC Shoah Archive), or Tübingen’s WebLicht services for data mining political and social science documents. CLARIN users don’t have access to the LAPPS Grid’s state-of-the-art tools for English and, through the LAPPS Grid’s federation with five Asian grids, to services providing a broad spectrum of capabilities for work in Asian languages. Scholars manually annotating a text corpus with CLARIN’s WebAnno (developed at TU-Darmstadt) would love to feed their work through iterative machine learning and evaluation facilities in the LAPPS Grid—but can’t.

The new Mellon Foundation funding will enable the project team to make the two grids interoperable on three levels:

  • Infrastructural: While the LAPPS Grid and CLARIN are both committed to open data and software, they do provide secure access to licensed resources, including the vast majority of the language data available over the web. The team will create a “trust network” between the two services, enabling single-authentication sign-on;
  • Technical: The LAPPS Grid and CLARIN have different underlying architectures and data exchange formats. The team will map these architectures and formats onto one another, enabling communication between the two frameworks over the web;
  • Semantic: To combine differently curated datasets, the data needs not only to share or be converted into a common format, but must also share a vocabulary for describing basic linguistic structures (a common language ontology) that tells computers how to combine the data into meaningful statements. The project team will extend the common exchange vocabulary developed by the LAPPS Grid to the web services of both frameworks and implement a set of conversion services.

The project will dramatically extend the power and reach of both the European and American frameworks and put their combined resources at the direct disposal of scholars from a broad range of fields in the humanities and social sciences, without requiring them to be computer programmers. “It will effectively create an ‘internet of language applications’ for the everyday computer user,” explained Dr. Pustejovsky. “We’re going to give every scholar access to a toolkit that’s now only available to the largest corporations.”

 

Jadhav receives NARSAD Young Investigator Grant

Assistant Professor of Psychology Shantanu Jadhav has recently been named to receive a 2015 NARSAD Young Invesigator Grant from the Brain & Behavior Research Foundation. The $70,000 award will help allow the Jadhav lab to

investigate the physiological interactions between the brain’s hippocampal and prefrontal cortex regions that support learning and memory-guided behavior. The two structures are important for different aspects of memory formation, storage, and retrieval, and impaired hippocampal-prefrontal interactions have been implicated in neurological disorders related to cognition, including memory disorders and schizophrenia.

Casey Wade Receives Grant from ACS Petroleum Research Fund

prf_figure_CWadeAssistant Professor of Chemistry Casey Wade has been selected to receive a Doctoral New Investigator grant from the American Chemical Society Petroleum Research Fund for his proposal, “Metal-organic Framework Supported Pincer Complexes: Investigation of the Effects of Site Isolation and Secondary Environment.” The two year grant will support the development of improved heterogeneous catalysts for the production of petroleum-derived commodity and fine chemicals.   Wade and coworkers plan to incorporate reactive transition metal catalyst sites into the well-defined 3-dimensional porous structure of metal-organic frameworks (MOFs). While the porous MOF support can be used to tune and promote reactivity, the immobilization of catalytically active sites prevents undesired bimolecular decomposition pathways and facilitates catalyst separation, leading to greener and more sustainable catalytic processes.

Post written by Christine Thomas

Papaemmanouil gets NSF CAREER grant

Assistant Professor of Computer Science Olga Papaemmanouil has received a Faculty Early Career Development (CAREER) award from the National Science Foundation (NSF), a highly selective grant that the National Science Foundation awards to junior faculty members who are likely to become academic leaders of the future.

The research project funded by Olga’s CAREER grant (“Towards Extensible Performance Management for Cloud Data Services“) aims to a) develop declarative mechanisms that allow application developers to express custom performance criteria for data processing tasks and b) exploit the properties of these mechanisms to design extensible resource, workload and Service-Level-Agreement (SLA) management services for cloud databases.

The project also includes the design and development of XCloud, an extensible cloud-based platform that will unify these services into a usable cloud utility. The XCloud platform is expected to have a significant research and educational impact as it will act as a test-bed for new performance models and diverse performance management techniques for cloud databases facilitating research and innovation in the emerging domain.

The Faculty Early Career Development (CAREER) Program is a Foundation-wide activity that offers the National Science Foundation’s most prestigious awards in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organizations. Such activities should build a firm foundation for a lifetime of leadership in integrating education and research.

Olga received her B.S. in Computer Engineering from the University of Patras, Greece, and completed her Ph.D. in Computer Science at Brown University in 2008. She joined the Computer Science Department at Brandeis in January 2009.

Other Brandeis science faculty receiving CAREER grants since 2010 include Christine Thomas (Chemistry), Aparna Baskaran, Matthew Headrick, and Zvonimir Dogic (all Physics).

2013 Sprout Grant Deadlines Announced

Call for Applications
3rd Annual Brandeis
University Virtual Incubator
“Sprout Grants”

The Brandeis University Virtual Incubator invites members of the Brandeis Community (undergrads, grad students, postdoctoral fellows, faculty, staff) to submit an application for a “Sprout Grant”.  These grants are intended to help entrepreneurs launch their research and ideas from the lab to the market. This spring, $50,000 will be shared among the most promising proposals.

Information sessions
  • Feb 6, 2 p.m.
  • Feb 8, 10 a.m.
  • Feb 11, 2 p.m.
Deadlines for this competition:
  • Preliminary Proposal: February 15, 2013
  • Full Application: March 8, 2013
  • Judging Event: April 15, 2013

Information sessions will be held in the Shapiro Science Center 1st floor conference room (Rm 1-09) at the following dates and times:

For more information email nborman at brandeis dot edu

The Brandeis University Virtual Incubator supports entrepreneurship through educating, mentoring, networking, and sponsoring. It is sponsored by the Brandeis University Office of Technology Licensing, and funded by the Office of the Provost.

Math graduate student training grant renewed

Mathematics Ph.D. students and faculty at Brandeis should be happy to learn that the department’s training grant from the US Dept. of Education’s Graduate Assistance in Areas of National Need (GAANN) program is being renewed for another three years. Training grants are a vital piece of the puzzle for supporting graduate education in the sciences, allowing Ph.D. students to focus on research.

 

NIH fellowships for Kuzirian and Ghiretti support neural development research

Marissa Kuzirian and Amy Ghiretti, graduate students in the lab of Dr. Suzanne Paradis, were each recently awarded Ruth L. Kirschstein National Research Service Awards for Individual Predoctoral Fellows (F31s) from the National Institutes of Health. Marissa’s 2.5-year award from the National Institute of Neurological Disorders and Stroke funds research to explore the role of Semaphorin4D and its receptor, PlexinB1, in regulating inhibitory synapse development and ultimately setting up proper neural connections in the mammalian CNS. Amy’s 2-year award from the National Institute on Drug Abuse funds a collaborative project between the Paradis, Lau, and Van Hooser labs here at Brandeis to elucidate the function of Rem2 in mediating experience-dependent changes in dendritic morphology in a living, intact animal system.

The basis for Marissa and Amy’s work comes from research into neurodevelopmental disorders such as Autism Spectrum Disorders (ASDs), as well as drug abuse and addiction. Proteins that regulate neurodevelopmental processes such as synapse development and dendritic morphology are important in both neurological disorders and drug addiction. Proper communication between neurons depends on the precise assembly and development of synaptic connections. The transmembrane protein Semaphorin4D (Sema4D) is necessary for proper GABAergic synapse formation, as knockdown of expression in the postsynaptic neuron by RNAi leads to a decrease in GABAergic synaptic density in cultured neurons (Paradis et al 2007). Marissa’s work will further explore this role of Sema4D in GABAergic synapse development.

Inhibitory synapses are identified in white along dendrites of a rat hippocampal neuron. Synapses are defined as sites of overlap between the postsynaptic protein GABAA receptor subunit γ2 (red) and the presynaptic protein GAD65 (blue) visualized by immunostaining. Neurons are visualized by immunostaining for MAP2 (green).

Marissa’s preliminary results demonstrate that adding the soluble, extracellular domain of Sema4D to cultured hippocampal neurons is sufficient to drive GABAergic synapse formation. This increase depends on the expression of Sema4D’s receptor, PlexinB1. Thus, Marissa’s work defines PlexinB1 as a novel receptor mediating GABAergic synapse formation in response to Sema4D in the mammalian CNS. The goal of Marissa’s project is to elucidate the role of Sema4D and its receptor, PlexinB1, in GABAergic synapse development. In experiments she proposed, she hypothesizes that Sema4D acts to initiate assembly of GABAergic synaptic proteins such as GABAA receptors and gephyrin through its receptor PlexinB1. This will be tested using a variety of imaging techniques in cultured hippocampal neurons, including confocal and time-lapse imaging, to measure the mobility and accumulation of GABAergic synaptic proteins in neurons after treatment with soluble Sema4D. The experiments will not only greatly expand our understanding of a novel receptor-ligand pair in GABAergic synapse development, it will inform as to some of the basic mechanisms underlying GABAergic synaptogenesis.

Molecular mechanisms, such as the Sema4D-PlexB1 interaction described above, are critical for the ability of the central nervous system (CNS) to respond to extracellular stimuli and make corresponding changes in the structure and function of a neuron. At the behavioral level, this plasticity allows an organism to respond to a changing environment appropriately in order to survive. At the level of individual neurons, this is reflected in changes in gene expression that occur in response to a variety of stimuli, including alterations in neuronal network activity. The goal of Amy’s work is to characterize a direct molecular link between changes in neuronal activity and changes in dendritic morphology.

A neuron in the optic tectum of a Xenopus tadpole; Green Fluorescent Protein expression allows the dendrites to be visualized.

Amy has previously implicated the protein Rem2, a type of signaling molecule known as a GTPase, as a mediator of such neurodevelopmental processes as excitatory synapse formation and dendritic morphology (Ghiretti & Paradis 2011). The expression of Rem2 in individual neurons is upregulated following increased neuronal activity, suggesting that it may serve as a direct link between changes in activity and corresponding changes in the structure and function of neurons. Her recently funded work will utilize Xenopus laevis tadpoles to study the effects of visual experience (by exposing the tadpoles to a light stimulus) on Rem2 expression, and in turn, how Rem2 mediates experience-dependent changes in the morphology of neurons in a region of the brain known as the optic tectum, where visual processing takes place. Ultimately, a full understanding of how Rem2 functions to shape the morphology of neurons in an intact system may help to inform knowledge of how the human brain changes as a result of neurological disorders or drug abuse, and aid in the development of more effective treatments to prevent these changes from occurring.

2012 Sprout Grant Competition Announced

C:\Documents and Settings\morgens\Local            Settings\Temporary Internet            Files\Content.IE5HQHO5IR\MC900437615[1].wmfCall for Applications

2nd Annual Brandeis University Virtual Incubator

“Sprout Grants”

The Brandeis University Virtual Incubator invites members of the Brandeis Community (undergrads, grad students, postdoctoral fellows, faculty, staff) to submit an application for a “Sprout Grant”.  These grants are intended to help entrepreneurs launch their research and ideas from the lab to the market. This spring, $50,000 will be shared among the most promising proposals.

Deadlines for this competition:

  • Preliminary Proposal:  February 10, 2012
  • Full Application:  March 9, 2012
  • Judging Event:  end of March

Information sessions will be held in the 4th floor conference room in the Ros-Kos Connector at the following dates and times:

  • Jan 24, 11 a.m.
  • Jan 31, 11 a.m. 
  • Feb  2, 10 a.m.
  • Feb  7,  10 a.m.
  • Feb  9,  11 a.m.

For more information and an application, contact Irene Abrams at iabrams@brandeis.edu

The Brandeis University Virtual Incubator supports entrepreneurship through educating, mentoring, networking, and sponsoring. It is sponsored by the Brandeis University Office of Technology Licensing, Irene Abrams, Associate Provost for Innovation, and funded by the Office of the Provost.

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