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This post is about two things. The first topic is a style of formalization in Agda that Bernardo Toninho and I picked up on from Dan Licata. The second topic is a way of establishing termination arguments that Bernardo and I worked out and used extensively in the Agda formalizaiton of several variants of Constructive Provability Logic, which I've mentioned before. Because I'm a bit perverse, I'll be using my own Agda Standard Library as the basis for this post; the code for this post can be found here - since it's a demo bound together with my library, technically I guess I'm supposed to keep the file at that link (though maybe not this post) in sync with the library as the library evolves.
Starting point: the simply-typed lambda calculusThis is a pretty standard Agda formalization of "Church-style" simply-typed lambda calculus terms. "Church-style," as opposed to "Curry-style," encodings only allow for the existence of well-typed terms.*
open import PreludeThe only non-obvious part of this encoding is that variables are represented by "dependent de Bruijn indices" - instead of a de Bruijn index being just a natural number, it's the pointer into its type in the context. The nice part about doing it this way is that you can define a very powerful notion of "generalized weakening" that is based on the "subset" partial order on contexts (Γ ⊆ Δ is a function mapping all the indices A ∈ Γ to indices A ∈ Δ).
infixr 5 _⊃_
data Type : Set where
con : String → Type
_⊃_ : Type → Type → Type
Ctx = List Type
infixl 5 _·_
data Term (Γ : Ctx) : Type → Set where
var : ∀{A} → A ∈ Γ → Term Γ A
_·_ : ∀{A B} → Term Γ (A ⊃ B) → Term Γ A → Term Γ B
Λ : ∀{A B} → Term (A :: Γ) B → Term Γ (A ⊃ B)
_⊆_ : Ctx → Ctx → SetThe nice part about this definition, and one of the things I picked up on from Dan, is that we can then define the usual weakening, exchange, and contraction properties directly by using generalized weakening and the corresponding facts about the subset relation on lists (which are defined in my standard library).
_⊆_ = LIST.SET.Sub
wk : ∀{Γ Δ A} → Γ ⊆ Δ → Term Γ A → Term Δ A
wk θ (var n) = var (θ n)
wk θ (n1 · n2) = wk θ n1 · wk θ n2
wk θ (Λ n) = Λ (wk (LIST.SET.sub-cons-congr θ) n)
wken : ∀{Γ A C} → Term Γ C → Term (A :: Γ) CWith that out of the way, we can talk about substitution, both the "obvious way" and the metric-indexed way Bernardo and I have used extensively.
wken = wk LIST.SET.sub-wken
exch : ∀{Γ A B C} → Term (A :: B :: Γ) C → Term (B :: A :: Γ) C
exch = wk LIST.SET.sub-exch
cntr : ∀{Γ A C} → Term (A :: A :: Γ) C → Term (A :: Γ) C
cntr = wk LIST.SET.sub-cntr
Straightforward substitutionThe obvious (for some value of obvious) and direct definition of substitution involves 1) generalizing the induction hypothesis to allow for even more additions (tm-subst) and 2) writing a variable substitution lemma that handles the case where the substituted-into term is a variable and we either perform the substitution, lower the de Bruijn index, or leaving the de Bruijn index alone (var-subst). The main theorem is inductive on the structure of the first term.
subst : ∀{Γ A C} → Term Γ A → Term (A :: Γ) C → Term Γ CTo motivate the next step, I'll point out that the only reason we had to generalize the induction hypothesis is because of the lambda case - if we try to prove the theorem directly, we find ourselves in the position of having a Term Γ A and a Term (B :: A :: Γ) C; we can't apply the induction hypothesis directly on these two terms. We can apply wken to the first subterm and apply exch to the second subterm and call subst recursively, but now we can't establish termination on the structure of the second term, since we've passed it to the exch function, which changed its structure by replacing Zs with (S Z)s and vice versa.
subst = tm-subst [] _
var-subst : ∀{A C} (Γ Γ' : Ctx)
→ Term Γ' A
→ Term (Γ ++ Γ') C
var-subst [] Γ' n1 Z = n1
var-subst [] Γ' n1 (S n) = var n
var-subst (_ :: Γ) Γ' n1 Z = var Z
var-subst (_ :: Γ) Γ' n1 (S n) = wken (var-subst Γ Γ' n1 n)
tm-subst : ∀{A C} (Γ Γ' : Ctx)
→ Term Γ' A
→ Term (Γ ++ [ A ] ++ Γ') C
→ Term (Γ ++ Γ') C
tm-subst Γ Γ' n1 (var n) = var-subst Γ Γ' n1 n
tm-subst Γ Γ' n1 (n · n') = tm-subst Γ Γ' n1 n · tm-subst Γ Γ' n1 n'
tm-subst Γ Γ' n1 (Λ n) = Λ (tm-subst (_ :: Γ) Γ' n1 n)
Setting up a metricThe alternate solution I intend to present involves setting up a metric; this metric expresses the "shape" of a term, disregarding all binding. This is a three-step process: first we define a generic "tree" piece of data that can capture the shape of a term (disregarding binding), and second we define a copy of the Term datatype, called MTerm, that has a Metric as one of its indices.
data Metric : Set whereThe third step is to show that we can freely get into and out of the metric; potentially we should also show that these two actions are an isomorphism, but I haven't run across the need to actually prove that. It really turns out that Agda does most of the work here...
○ : Metric
_●_ : Metric → Metric → Metric
> : Metric → Metric
data MTerm (Γ : Ctx) : Type → Metric → Set where
var : ∀{A} → A ∈ Γ → MTerm Γ A ○
_·_ : ∀{A B m m'} → MTerm Γ (A ⊃ B) m → MTerm Γ A m' → MTerm Γ B (m ● m')
Λ : ∀{A B m} → MTerm (A :: Γ) B m → MTerm Γ (A ⊃ B) (> m)
tm→ : ∀{Γ A m} → MTerm Γ A m → Term Γ ANow that we have our metric, we can prove a stronger and more useful version of the generalized weakening lemma: not only can we apply generalized weakening to terms, but the resulting term has the exact same shape (as shown by the fact that the same metric "m" appears as an index both to the function's argument and its conclusion.
tm→ (var n) = var n
tm→ (n1 · n2) = tm→ n1 · tm→ n2
tm→ (Λ n) = Λ (tm→ n)
→tm : ∀{Γ A} → Term Γ A → ∃ λ m → MTerm Γ A m
→tm (var n) = , var n
→tm (n1 · n2) = , snd (→tm n1) · snd (→tm n2)
→tm (Λ n) = , Λ (snd (→tm n))
wkM : ∀{Γ Δ A m} → Γ ⊆ Δ → MTerm Γ A m → MTerm Δ A mWe don't need to prove weakening twice; our previous weakening lemma is just a simple consequence of this new, stronger one:
wkM θ (var n) = var (θ n)
wkM θ (n · n') = wkM θ n · wkM θ n'
wkM θ (Λ n) = Λ (wkM (LIST.SET.sub-cons-congr θ) n)
wk : ∀{Γ Δ A} → Γ ⊆ Δ → Term Γ A → Term Δ A
wk θ n = tm→ (wkM θ (snd (→tm n)))
Substitution with the metricWith the metric in tow, substitution is straightforward. Termination is established by induction on the metric of the second term. Note the use of both wken (weakening outside of the metric) and exchM (exchange inside the metric) in the lambda case.
subst : ∀{Γ A C} → Term Γ A → Term (A :: Γ) C → Term Γ CIn this example, it's not clear that we've saved much work: setting up the metric was a lot of boilerplate, though it is straightforward; the benefit that we gained in terms of proof simplicity was primarily an artifact of Agda's pattern matching: either a variable was the first variable in the context (and therefore represented by the de Bruijn index Z), or it was later in the context. So this example isn't the world's best argument for this style, but in the more complex logics that Bernardo and I dealt with, we found that this technique seemed, of all the approaches we could think of, to be the one least likely to fail on us.
subst n1 n2 = substM n1 (snd (→tm n2))
substM : ∀{Γ A C m} → Term Γ A → MTerm (A :: Γ) C m → Term Γ C
substM n1 (var Z) = n1
substM n1 (var (S n)) = var n
substM n1 (n · n') = substM n1 n · substM n1 n'
substM n1 (Λ n) = Λ (substM (wken n1) (exchM n))
CommentsDan's said on a couple of occasions that he thinks there are less painful ways of doing this sort of thing, existing Agda techniques that avoid the annoying duplication of data types. My understanding is also that there is a not-totally-integrated notion of "sized types" in Agda that could maybe handle this sort of thing, but that the way it works is by defining metrics that are only natural numbers. It seems like a step backwards, somehow, if we go from structural induction to natural number induction. Furthermore, sized types based on natural numbers would almost certainly fail to handle the vaguely insane termination arguments that come up in constructive provability logic.
Totally nameless representations?The germ of this post comes from a conversation with Chris Casinghino at UPenn back in May. He was working on extending this sort of simple representation in a way that was similarly-insane but mostly unrelated to constructive provability logic. Our problems were different; he placed the blame for some of the difficulties he encountered on the "sillyness of using all de bruijn indices instead of a locally nameless encoding," which was a response that I initially found puzzling. I've since decided that my puzzlement was the result of the fact that he was thinking of the specific thing he was doing in terms of programming languages, and I was thinking about the thing I was doing (constructive provability logic) in terms of logic - my guess is that we're both so used to working on both sides of the Curry-Howard correspondence that it wouldn't have occurred to us that this might make a difference!
From a programming languages perspective, we have programs and typing derivations that show programs to be well typed; the locally nameless encoding gives you the ability to apply the exchange or weakening lemma and get a new typing derivation that says that the same term is still well typed. That wasn't the case for our original "Church-style" lambda calculus terms. In my current view, that's because a "Church-style" lambda calculus term is more like the typing derivation than it is like a term. It's a typing derivation without the term it's typing; in other words, it's a proof in natural deduction form! And what Bernardo and I was using was something that, for our purposes, was just as good as a derivation that the same term was well typed in the exchanged context - we got that the same metric was associated with the exchanged proof term.
In other words, it seems that, for the purposes of termination arguments, the metric serves the same purpose a locally nameless proof term does. Certainly it avoids the "silliness of using all de Bruijn indices," as it uses none whatsoever, hence the mostly-joking title of this post. However, it's quite possible I'm off base; I'd be interested in what people more versed in locally nameless representation thought. I should add that I certainly think it is possible to do an intrinsically typed locally nameless representation; you'd just have to have (at minimum) the free variables be aware of their type. If you were interested primarily in representing a programming language that might even be the right thing to do; but the totally nameless metrics seem to be an easier fit for developments where the primary interest is in the logic side of the correspondence.
* Shameless plug for my advisor Frank Pfenning's excellent essay, "Church and Curry, Combining Intrinsic and Extrinsic Typing" which talks about properties of Church-style versus Curry-style encodings and relates them to subtyping and work by William Lovas.
P.S. This blog post has been about Agda; the first time I used this kind of tree structural metric on terms was in Twelf, when (on a challenge from John Boyland) I showed a bijection between HOAS and de Bruijn form representations of the terms of an untyped (or, if you prefer, "Curry-style") lambda calculus terms.


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November, 2009
Americans for the Arts
Americans for the Arts (AFTA) is dedicated to representing and serving local communities and creating opportunities for every American to participate in and appreciate all forms of the arts. AFTA has offices in Washington, D.C., and New York and has more than 5,000 organizational and individual members. Local arts agencies comprise the core constituency. A variety of partner networks are also supported. The Web site offers a broad overview of their field services, including an arts and education network, public art, united arts funds, and emerging leaders.
ArtsEdge was developed more than ten years ago through a cooperative agreement among the U.S. Department of Education, the National Endowment for the Arts, and the John F. Kennedy Center for the Performing Arts. This online resource center aims to connect people, provide resources, and build a new base of knowledge in the area of arts education. To achieve these goals, ArtsEdge offers teaching materials, resources for advocacy, and media-rich, student-friendly activities.
Arts Education Partnership
Arts Education Partnership (AEP) is a national coalition of arts, education, business, philanthropic, and government organizations that demonstrate and promote the essential role of the arts in the learning and development of every child and in the improvement of America's schools. AEP was formed in 1995 through a cooperative agreement among the National Endowment for the Arts, the U.S. Department of Education, the National Assembly of State Arts Agencies, and the Council of Chief State School Officers. AEP's Web site contains resources for partnerships, a state policy database, a research compendium, evaluation and assessment information, publication tool kits, a library of arts-integration programs, and publications that can be easily accessed or ordered.
The Dana Foundation
The Dana Foundation provides the latest information on brain research, arts education, and neuroeducation. The foundation offers free books and publications, including Brain in the News and Arts Education in the News, Transforming Arts Teaching, Learning, Arts, and the Brain, and this publication. A Webcast of the release of the Dana Arts and Cognition Consortium findings is available on the Web site.
Edutopia, a print and online magazine created and maintained by The George Lucas Educational Foundation, is dedicated to promoting positive change in education. The Web site offers interactive resources, advice, examples, and contributions from practitioners. An archive of best practices is maintained for all education stakeholders. Of particular interest is the arts-education section, which contains articles, blog posts, videos, and slide shows of the latest in arts-education news.
Grantmakers in the Arts
Grantmakers in the Arts is a membership organization focused on arts philanthropy discourse within a diverse community of grantmakers. Members include private, community, corporate, and family foundations, as well as public sector grantmakers, regranting organizations with the primary purpose of arts grantmaking, and individual donors who give through eligible organizations. GIA programs include an annual conference, a major periodical, research, and other convening and communication services.
Keep Arts In Schools
In August 2007, Douglas Gould and Company launched keepartsinschools.org, funded by the Ford Foundation. The Web site includes the latest news, events, case studies, research, and hands-on advocacy support in the form of sample letters, petitions, and testimony, highlighting the efforts of arts-education organizations throughout the country and making tools and resources available to those seeking to make the arts top priority in public schools and communities.
Lincoln Center Institute
Founded in 1975, the Lincoln Center Institute (LCI) is the educational cornerstone of the Lincoln Center for the Performing Arts, Inc., and a global leader in education and the arts. Since its inception, LCI has reached over three million students and some 50,000 educators. Students learn about and through the arts by focusing on works of art, including performing arts, visual arts, and architecture. The Institute works in partnership with pre-K-12 educators and degree-granting teacher-education programs, and provides numerous professional-development opportunities.
MENC: The National Association for Music Education
The mission of MENC is to "advance music education by encouraging the study and making of music by all." MENC's Web site contains links to resources that discuss the benefits of arts education for "success in society, success in school and learning, success in developing intelligence, and success in life."
National Assembly of State Arts Agencies
The National Assembly of State Arts Agencies (NASAA) is a membership organization that unites, represents, and serves the nation's state and jurisdictional arts agencies. NASAA's mission is to advocate and promote a meaningful role for the arts in the lives of individuals, families, and communities throughout the United States. NASAA's Web site offers links to every state arts agency, major grantmakers in arts and culture, arts and learning resources, and to information about cultural tourism policy, creative economy, and arts as a public policy asset.
National Endowment for the Arts
The National Endowment for the Arts (NEA) is a public agency dedicated to supporting excellence in the arts, both new and established; bringing the arts to all Americans; and providing leadership in arts education. NEA was established by Congress in 1965 as an independent agency of the federal government and is the largest public funder of the arts, bringing art to all 50 states, rural areas, inner cities, and military bases. The NEA provides funding through a variety of discipline-specific program areas, as well as for special national initiatives. The NEA's Web site highlights each funding area and the opportunities therein.
Neuro-Education Initiative
Located at the Johns Hopkins University School of Education, the Neuro-Education Initiative (NEI) bridges the gap between the brain sciences and education by bringing together an interdisciplinary group of researchers, educators, and other key stakeholders to explore the intersection, knowledge, and current application of brain research in education, and to identify and support potential areas of translational research.
Project Zero
Project Zero is a research group at the Harvard Graduate School of Education. Its mission is to understand and enhance learning, thinking, and creativity in the arts, as well as humanistic and scientific disciplines, at the individual and institutional levels. Project Zero has maintained a firm research commitment in the arts, and has gradually expanded to include education across all disciplines. Its work is documented extensively on its Web site through a variety of publications, papers, and articles. Artful Thinking, a program developed by Project Zero in collaboration with the Traverse City, Michigan Area Public Schools, aims to develop a model approach for integrating art into classroom instruction. Its Web site (http://www.pz.harvard.edu/tc) contains lesson plans and resources for K-6 classroom teachers.
State Education Agency Directors of Arts Education
The State Education Agency Directors of Arts Education (SEADAE) supports the professional effectiveness of individual members and provides a collective voice for leadership on issues affecting arts education. Its purpose is to achieve quality, comprehensive, sequential, standards-based arts education for all pre-K-12 students. SEADAE identifies and responds to key issues in arts education, strengthening arts-education policy at national and state levels, and maintaining a network to exchange ideas and information. It also collaborates with other organizations to support vision and leadership in arts education. SEASAE is supported by NASAA and the NEA.
UC Irvine Center for Learning Through the Arts and Technology
The Center for Learning Through the Arts and Technology brings together faculty and researchers from various departments within UC Irvine to "study the reciprocal impact of the arts on the Center's focus areas, including the formulation of new public policy." Its Web site features several articles that relate arts and learning.
U.S. Department of Education and the Office of Innovation and Improvement
The U.S. Department of Education promotes student achievement and preparation for global competitiveness by fostering educational excellence and ensuring equal access. Key aspects of the Department of Education's focus include collecting data on America's schools, disseminating research, and focusing national attention on key educational issues. Together with the National Institute of Education, the U.S. Department of Education sponsors the Educational Resources Information Center (ERIC), which provides free access to more than 1.2 million citations on education topics.
The Office of Innovation and Improvement (OII) makes strategic investments in innovative educational practices through discretionary grant programs. It coordinates public school choice and supplemental educational service provisions of the Elementary and Secondary Education Act, as amended by No Child Left Behind.
Young Audiences Arts for Learning
Young Audiences, Inc. is a nationwide arts-education programming and service organization. Arts for Learning is a supplemental literacy program that brings together students, classroom teachers, and teaching artists to engage in arts-integrated literacy learning. The Web site offers a keyword search for best practices in arts education and a Web library of curricula developed at schools and organizations across the country.
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subset: commoncrawl


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Engineering in Medicine
Behind every great medical advance, there's a great engineer.
By Elizabeth Kelsey
Photographs by John Sherman
Anyone who goes to the doctor benefits from the work of engineers. Every medical device represents a collaboration between doctors eager for better ways to treat patients and engineers eager to push technological boundaries. Dartmouth engineers have focused on medical technologies since the 1960s, when Professor John Strohbehn started a biomedical engineering program at Thayer. Collaborating with clinicians at Dartmouth Medical School, Strohbehn directed his inventive skills to a wide range of medical applications, including mathematical models for X-ray tomography, an interactive image processor for clinical use, hyperthermia techniques for destroying cancer cells with heat, and a frameless stereotactic operating microscope for neurosurgeons. His work inspired several graduate students who today are lead researchers at Thayer, including Professor Stuart Trembly Th'82, who developed a microwave thermokeratoplasty technique to correct nearsightedness, and Keith Paulsen Th'86, who heads the engineering side of Dartmouth's comprehensive medical imaging programs.
Thayer School is home to a wide range of medical projects. Some, such as the joint implant work of professors John Collier '72 Th'77, Douglas Van Citters '99 Th'03, '06, and Dr. Michael Mayor, have led to major improvements in medical devices and techniques. Others have resulted in new companies, such as GlycoFi, the protein engineering start-up that professors Tillman Gerngross and Charles Hutchinson sold to Merck in 2006 for $400 million, or Gerngross' latest bioengineering venture, Adimab.
In the following, Dartmouth engineers explain some of the many projects they are working on with colleagues at Dartmouth Medical School and Dartmouth-Hitchcock Medical Center to give doctors new tools for better care.
The Researcher: Professor Ursula Gibson '76
Nanomedicine is the intersection between nanomaterials and medical research. We're using knowledge of self-assembly of small-scale materials to try to make therapeutic substances that will interact with diseased tissue.
Cancer tissues have a vasculature that is not well developed. They essentially have little pores in them that are about 300 nanometers in diameter — a scale at which people have started to gain control over what they can fabricate. The leaky vasculature allows us to preferentially deposit nanoparticles inside a tumor.
If we can structure materials on a very fine scale, we can give them a plethora of functionalities for targeting cancer. We could incorporate a drug into a polymer structure, add some magnetic nanoparticles that can absorb energy from an externally applied field, and attach an antibody to the outside of the polymer to help it find the cancer or bind preferentially to the cancer for a multiplicative effect.
There's a lot of work now to figure out how to get therapeutic drugs and materials into tumors without having them intercepted by the body's natural defenses, how to optimize entrance into the tumor, and how to activate the drugs and materials once they get there. There are certain conditions that are present in a tumor — the pH is different, the oxygen concentration is different — and people would like to leverage all of those into a system that gives a higher release factor in cancerous regions and a lower release anywhere else.
The Researcher: Professor Ian Baker
You can heat up nanoparticles by applying an alternating magnetic field. If you introduce the particles into a tumor — either by injecting them or by antibody-tagging them — you can use the heat to kill cancer cells.
Many groups have been working on using iron-oxide particles for magnetic hyperthermia. We're making iron nanoparticles coated with iron oxide. We wanted to use iron because it is more magnetic — and therefore has greater heating abilities — than iron-oxide. But nano-sized iron particles exposed to air quickly form an oxide and produce so much heat that they catch fire. I had the idea of using iron particles for their heating effect and coating them with iron oxide to make them safe and make them visible in magnetic resonance imaging. But I really hadn't much clue how to do it. Fortunately, post-doc Qi Zeng figured it out. More recently another post-doc, Guandong Zhang, managed to tweak the processing so that now our particles range from 8 to 20 nanometers, heat well, have a biocompatible coating, and have good MRI contrast.
The ultimate goal is to tag these nanoparticles with tumor-specific antibodies, and put them into the bloodstream to find their way to a tumor and attach to it. Then, using a technique like MRI to ensure the particles are at the tumor, we'll magnetically heat the tumor to destroy it without damaging surrounding tissue.
The Researcher: Professor Kofi Odame
Low-power electronics are crucial for medical devices that need to be portable or implantable.
A cochlear implant works by capturing sound, processing it, and — bypassing the inner ear — stimulating the patient's auditory nerve. Currently only a small part of the device is actually implanted. An external part contains a microphone, microprocessor, and batteries, which need to be replaced or recharged every 24 hours or so.
I want to make an implant that will allow users to discriminate between sounds they're interested in hearing — say a conversation — and background noise. I'm currently working on an algorithm and designing an electronic circuit that will imitate a healthy cochlea.
But a fully internal cochlear implant, with all of its parts surgically placed inside the patient's head, will never become a reality unless the implant is made to consume so little power that batteries would only need to be changed once every several years, if at all.
Many people with epilepsy need to be monitored long-term. Monitoring in hospitals is expensive and disruptive. Portable EEG monitors exist, but they're bulky and awkward. My idea is to create a device that is small enough to fit in a hat. The device would be doing wireless transmission of electroencephalogram (EEG) data, which consumes a lot of power. I'm designing circuits that selectively transmit only the important portions of EEG data in a low-power fashion.
The Researcher: Professor John Collier '72 Th'77
We look at the problems orthopedists and patients have with hip and knee implants and figure out how to solve them.
It used to be that loosening of implants was a big problem. Loosening is no longer a problem [thanks largely to a porous coating Collier developed in the 1980s]. It used to be that a success rate of 70–80 percent at five years was good. Now it's 97–99 percent at ten years. We're looking to push that to 97–99 percent at 20 years or more.
But making better materials for implants is tough. People use implants in a very active environment over many years. We do in-vitro simulations, but when a new material is put in the body, we commonly get surprised. The body environment is complicated — with proteins, enzymes, free radicals, cells, low pH, and a whole lot of other things going on — and implants are submersed in it for a long time. We don't know how to model all those conditions.
Orthopedic surgeon Michael Mayor thought that if we're putting implants into patients, we ought to examine the devices when they come out. He started our implant retrieval lab. Since the 1970s he has evaluated nearly 10,000 retrieved implants for corrosion and other damage. We compare components that have been in patients to predictions from our tests. There's a constant evolution of tests and evaluation of components.
Cross-linked polyethylene components show promise. Polyethylene is a long-chain monomer; you can improve its wear resistance by connecting the chains to one another.
Even with a sophisticated prosthetic device, surgeons can get into difficulty if they haven't done many implant procedures. The device might not be exactly the right size or it might not be tensioned or positioned exactly. Any one of those things is sufficient to cause the device to fail. It's very difficult to make devices robust enough to survive if they're put in the wrong position.
The Researcher: Professor Solomon Diamond '97 Th'98
My graduate students and I want to understand how neurodegenerative diseases like Alzheimer's work, so we're developing brain imaging tools and technologies to dynamically measure neurovascular coupling — the relationship between evoked neural activity and subsequent changes in cerebral blood oxygen, volume, and flow.
We're building a special brain imaging lab at Thayer that will allow us to run three different noninvasive neuroimaging techniques simultaneously. One technique is electroencephelography (EEG), which measures electrical potentials on the scalp that arise from ionic currents in the brain's neurons; the second is magnetoencephelography (MEG), which measures the magnetic field around the head that also comes from neural currents; the third is near-infrared spectroscopy (NIRS), which uses near-infrared light to rapidly measure brain blood volume and oxygen dynamics.
Our instruments will allow us to explore neurovascular relationships with more precise timing and better specificity to neural currents than can be done with an MRI. With functional MRI, you get an image stack of the whole brain about every two seconds, and you can see how the stack evolves over time due to the cerebral blood dynamics. You can tell what part of the brain was active when the subject saw a certain stimulus or performed a particular task. But you wouldn't know the moment-to-moment waveform of blood dynamics, and you wouldn't have any concurrent measure of the neural currents. We will be able to measure cerebral blood and neural dynamics in our lab.
Once all the instruments are functioning, we'll start studying the neurovascular coupling relationships in healthy normal controls. With that data as a foundation, we can then begin the pilot clinical work, measuring people who are at risk for developing Alzheimer's or who are in the early stages of it. The background work could take five years, but I envision early clinical work at the pilot level starting in two to four years.
The Researcher: Professor Karl Griswold
I think of proteins as the nanoscale machines that enable life. Knowing how well proteins work in their natural context, engineers and scientists have envisioned ways in which we can use these molecules to enable practical applications. However, when you yank proteins out of their natural context, they frequently lose some or all of their desirable qualities. This is where protein engineering comes into play. We take natural protein sequences as a starting point and redesign them to meet our own performance criteria.
Seeing proteins as next-generation antibiotics, I wanted to develop enzymes to treat bacterial infections. That led me to work on cystic fibrosis.
Most CF patients die from complications associated with Pseudomonas aeruginosa bacterial infection of the lungs. In many infections, bacteria adhere to a surface — such as the lining of the lung, a catheter, or an orthopedic implant — and cover themselves with biofilm, a blanket of proteins, nucleic acids, carbohydrates, and other components. By growing inside this complex matrix, bacteria gain protection from the human immune system and antibacterial drugs. This is what makes Pseudomonas in the lungs of CF patients so insidious. Once contracted, the bacteria generally cannot be eradicated.
We're looking for enzymes that will break through Pseudomonas' biofilm armor. We're identifying natural enzymes that have infection-fighting potential, outlining their limitations, and then developing improved versions in the lab.
Mammography isn't perfect. That's why Thayer School engineers and Dartmouth Medical School (DMS) researchers have been working together for a decade on four alternative imaging technologies to detect and help treat breast cancer.
Keith Paulsen Th'84, Thayer School's Robert A. Pritzker Professor of Biomedical Engineering, and Dartmouth Medical School radiology professor Dr. Steven Poplak are the principal investigators. Together they lead a team of some 40 engineers, radiologists, pathologists, computer programmers, data analysts, and other collaborators who are refining the technologies and conducting clinical trials at Dartmouth-Hitchcock Medical Center.
The four technologies — microwave imaging spectroscopy (MIS), electrical impedance spectroscopy (EIS), near-infrared imaging (NIR), and magnetic resonance elasticity (MRE) — differ from mammography in a key way. Mammography detects tissue that looks like a tumor. The other technologies detect tissue that acts like a tumor.
MIS and EIS measure the ability of different regions of the breast to hold or conduct electricity. Part of what defines a tissue as cancerous is how its cells and blood vessels are organized. Normal tissue is quite orderly. Cancer, however, is "just a jumble," says Thayer professor Alex Hartov Th'88, EIS project leader. "A lot of membranes, a lot of vascularity — all these things are associated with different electrical properties."
NIR uses a "unique spectral window," says Thayer professor Brian Pogue, who leads the NIR project. Penetrating deep into tissue, NIR reveals information about hemoglobin and oxygen saturation levels, which can indicate a tumor.
MRE uses an MRI scanner and specialized coils to vibrate breast tissue and measure whether it is elastic or stiff. "Almost all cancer is stiff," says MRE project leader John Weaver, a professor of radiology at DMS and adjunct professor at Thayer.
All four technologies differ from mammography in another way as well: computational complexity. Since mammography utilizes X-rays, which penetrate the body in more or less a straight path, constructing an image from X-ray data is a relatively easy linear problem. But the electromagnetic waves used in MIS, EIS, and NIR and the mechanical waves generated during MRE travel through the breast in complex patterns. Generating images from this data requires complex differential equations.
The mathematical and engineering problems involved in getting these modalities to work are "huge," says Thayer professor Paul Meaney Th'95, head of the MIS project.
Even so, the Thayer-DMS group has developed both the software and the hardware — free-standing machines for MIS, EIS, and NIR, plus specialized equipment that's used inside an MRI scanner for MRE and NIR. And while researchers elsewhere are working on their own versions of the technologies, no program is as comprehensive and well developed as the Dartmouth collaboration.
"We're looking at all four technologies in a common setting," explains Paulsen. "We can look at them together and comparatively and synergistically."
Size is part of the success, says Paulsen. "It's sort of the big company/small company paradigm," he explains. A big company can't adapt itself quickly to something new, he says, "because there's huge infrastructure and huge investment in teams. We're a much more nimble, small enterprise."
—Jennifer Durgin
(Excerpted and adapted from "All Together Now," by Jennifer Durgin, published in Dartmouth Medicine. Used with permission.)
Thayer researchers explain new applications for their imaging technologies.
Professor Keith Paulsen Th'84
We're developing a fluorescence signature to guide surgeons in removing brain tumors. We've found that high-grade tumors fluoresce, so the fluorescence can be used as a kind of surgical road map. We hope to be able to make low-grade tumors fluoresce, too, so they can be treated before they get worse.
Professor Brian Pogue
Glioma brain tumors don't always show up in an MRI scan. The most problematic parts of a tumor cannot be seen structurally because they're a microscopic invasion. With better molecular tracers and optical imaging, though, we've been able to detect them. This is very exciting, because we can now demonstrate that we can see something that standard clinical imaging doesn't capture.
Our glioma research has been done on mouse models of human cancer. We use an injectable agent that isn't FDA-approved yet, but would be a good candidate for future clinical use. We need to do phase-one trials with new drugs and imaging systems to make sure they don't harm the patient. The process takes years and depends on funding, competing technologies, and other factors. If all the right factors come together, we can consider doing imaging studies on humans.
Professor John Weaver
We're using imaging to monitor neoadjuvant therapies to treat metastatic cancers. Rather than immediately removing the primary cancer, the oncologist leaves it in place and attacks it with a mix of chemotherapies. If the chemotherapies shrink the primary tumor, you can assume that they also attack unseen metastases. Obviously, you want to find out really quickly if the chemo cocktail is working. Instead of waiting a month, we want to use imaging to find out in a week.
Professor Paul Meaney Th'95
If you're using heat to destroy a tumor, you want to monitor the temperature during the treatment. It has been challenging to find a noninvasive method. We use a focused utrasound system to heat the tumors. We've integrated a microwave imaging system into it, allowing us to continuously image the patient while the heating occurs.
Professor Ryan Halter Th'06
A big problem with screening for prostate cancer is that the prostate-specific antigen (PSA) test is not specific to just cancer. Benign conditions can also cause PSA levels to rise. Ultrasound-guided biopsy is used to definitively diagnose prostate cancer in men with elevated PSA, but it misses some malignant lesions and doesn't accurately characterize the extent of the disease. We're incorporating electrical impedance spectroscopy (EIS) sensors into standard biopsy needles and ultrasound probes to improve this detection and disease characterization. We're also developing EIS-enhanced probes that surgeons can use during surgery to ensure clear margins.
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I have followed whatever the official documentation said about configuring DiffMerge for "Git for Windows (MSysGit)" - However when I am running "git difftool", the command silently returns without anything happening.
NOTE: When I first installed and configured DiffMerge for Git, the command "git difftool" did not silently return - instead there was pop which gave an error message that DiffMerge failed to launch. Then I was troubleshooting and tried many things - suddenly I found that "git difftool" command silently returns. Hence, I am not sure why this change happened!
I have tried both the MSI installer as well as the zip version - but nothing works in windows (however, notably things are working fine in Linux -Ubuntu) - the zipped version I used is "DiffMerge_4_2_0_697_stable_x64"
Also for example when I run the command: git config --global difftool.diffmerge.cmd "C:/Program\ Files/SourceGear/Common/DiffMerge/sgdm.exe \"$LOCAL\" \"$REMOTE\"" --and then run the command "git config --global --list", I can see the following entry in ".gitconfig" file corresponding to the command:
cmd = C:/Program\\ Files/SourceGear/Common/DiffMerge/sgdm.exe "" ""
Why are the LOCAL and REMOTE missing?
I tried to edit the .gitconfig directly by entering: cmd = C:/Program\\ Files/SourceGear/Common/DiffMerge/sgdm.exe \"$LOCAL\" \"$REMOTE\" in the .gitconfig file - still nothing worked.
"git difftool" doesn't launch DiffMerge
Support for our DiffMerge utility.
Moderator: SourceGear
14 posts • Page 1 of 1
Let's start with point 2, because I'm not sure what you mean by nothing working in Windows.
Are you able to launch DiffMerge separately from Git and use it? Once we've established that, then we can look at using it with Git.
Beth Kieler
SourceGear Technical Support
By "nothing working in Windows", I mean the following :
git config --global diff.tool diffmerge
git config --global difftool.diffmerge.cmd "F:/Bibhash/Programs/DiffMerge_4_2_0_697_stable_x64/sgdm.exe \"$LOCAL\" \"$REMOTE\""
git config --global merge.tool diffmerge
git config --global mergetool.diffmerge.trustExitCode true
git config --global mergetool.diffmerge.cmd "F:/Bibhash/Programs/DiffMerge_4_2_0_697_stable_x64/sgdm.exe /merge /result=\"$MERGED\" \"$LOCAL\" \"$BASE\" \"$REMOTE\""
STEP#2: HOW .gitconfig LOOKS
user.name=Bibhash Roy
difftool.diffmerge.cmd=F:/Bibhash/Programs/DiffMerge_4_2_0_697_stable_x64/sgdm.exe "" ""
mergetool.diffmerge.cmd=F:/Bibhash/Programs/DiffMerge_4_2_0_697_stable_x64/sgdm.exe /merge /result="" "" "" ""
STEP#3: After running the commands in step#1, I made some changes in a file called README.md (tracked) in the repo - I did not do "git add".
STEP#4: Then I ran "git diff" - as expected the inbuilt "diff" works fine!
STEP#5: Now I ran "git difftool" - I got the prompt "Launch 'diffmerge' [Y/n]" - pressed "Y" - It popped up an UI (in red cross symbol) with following error message "File () not found. File () not found."
QUESTION#1: Why I am getting this error message and why does DiffMerge fail to launch?
QUESTION#2: Why does the following variables - "$MERGED", "$LOCAL", "$BASE", "$REMOTE"" - show up as empty string ("") in .gitconfig file? Is this the source of error?
QUESTION#3: Why are the code/commands contain line-breaks in your documentation at https://sourcegear.com/diffmerge/webhel ... ysgit.html - the line breaks are very INCONVENIENT!
I need to resolve this problem quickly! PLEASE HELP! It is urgent!
Can you tell me the version of Windows you have?
Are you using a full Git install or the portable version on a thumbdrive?
I'm assuming you're using a command-line Git client. If that's not the case, then I'll need to know the name of the client you are using.
Beth Kieler
SourceGear Technical Support
OS I'm using: Windows 10 (licensed - regularly updated) 64 bit
DiffMerge Version I installed for Windows: Windows zip (64bit) DiffMerge 4.2 - tried Windows Installer (64bit) also
My Git installation: Full Git Installation - 64-bit Git for Windows Setup (git version 2.8.2) as available at https://git-scm.com/download/win (non-portable)
I also attached image of the error I am getting
Can you verify that you can run the DiffMerge tool itself? Let's make sure that works, and try to use it to diff the same files you're trying to Diff in Git.
Beth Kieler
SourceGear Technical Support
Yes I can run the DiffMerge executable (sgdm.exe) and I can do "diff" of same files that I was trying to use in GIT. Please, I need to resolve it quick...
DiffMerge now works on windows.....But.....read below:
Mistake I made
I installed the zipped version of DiffMerge and manually added this to PATH variable:
INSTEAD of this one:
Current Status
DiffMerge seems now works as desired BUT with a hack - read on.......
When I run the command: git config --global difftool.diffmerge.cmd "F:/Bibhash/Programs/DiffMerge_4_2_0_697_stable_x64/sgdm.exe \"$LOCAL\" \"$REMOTE\""
the entry in the .gitconfig looks like this:
[difftool "diffmerge"]
cmd = F:/Bibhash/Programs/DiffMerge_4_2_0_697_stable_x64/sgdm.exe \"\" \"\"
Note that the $LOCAL and $REMOTE is missing in the .gitconfig file - same thing happens for the related command for "merge"
Now I ran "git difftool" - this launched DiffMerge but the "diff" view was missing for the file I changed in the repository. So I did the following HACK - I modified the .gitconfig file so that the entry looks like this:
[difftool "diffmerge"]
cmd = F:/Bibhash/Programs/DiffMerge_4_2_0_697_stable_x64/sgdm.exe \"$LOCAL\" \"$REMOTE\"
Now "git difftool" command works fine and I can view the "diff" for the files I changed!!!
The hack I am using is unacceptable from my side and is only a temporary solution - I should be able to run the commands mentioned above without directly modifying the .gitconfig file. Please guide as to why the
\"$LOCAL\" \"$REMOTE\" e.t.c fails to appear in the .gitconfig file.......we are inching towards a solution...now I need your help to close this issue!!
What I have currently working with Windows 10 is the following entries in the .gitconfig:
tool = diffmerge
[difftool "diffmerge"]
cmd = C:/Program\\ Files/SourceGear/Common/DiffMerge/sgdm.exe \"$LOCAL\" \"$REMOTE\"
tool = diffmerge
[mergetool "diffmerge"]
trustExitCode = true
cmd = C:/Program\\ Files/SourceGear/Common/DiffMerge/sgdm.exe /merge /result=\"$MERGED\" \"$LOCAL\" \"$BASE\" \"$REMOTE\"
Then when I run a diff, I add the switch
This is the proper way to set up according to the manual here: http://www.sourcegear.com/diffmerge/web ... ithub.html
If you had a return before the local and remote, then those wouldn't be picked up and set.
Beth Kieler
SourceGear Technical Support
You said "If you had a return before the local and remote, then those wouldn't be picked up and set" - didn't quite understand what you meant by that. Do you mean "carriage return" when you say "return"? For me, the whole command is in a single line!
Note that I have NOT added the lines directly in .gitconfig (as said in the document you mentioned) - instead I ran the commands that would add the necessary lines in .gitconfig as given in the document https://sourcegear.com/diffmerge/webhelp/sec__git__windows__msysgit.html - so the question of adding a "return" does not arise.
Only reason, I feel, things are not working for me is that - $LOCAL, $REMOTE e.t.c are not getting set in .gitconfig though I am mentioning it in the command line.....
Can you tell me why this is happening?
If I do not get the right solution from you today, I have to stop experimenting with DiffMerge and instead switch to a different tool like p4merge
I apologize for any confusion this may have caused.
It looks like one needs to escape out the $ as well. The Cygwin instructions has the $ escaped. That means you can use the instructions for either Github or cygwin. It doesn't looks to me like you're using MySysGit, which is the instructions you posted that you were using.
Your screenshot is showing me Git Bash (git-bash.exe), which comes from the same link you posted. Is that what you're using?
The instructions for MySysGit should be run for Git Cmd (git-cmd.exe). The instructions for Cygwin should be run for Git Bash (git-bash.exe)
We can update the instructions to show Git Bash and Git Cmd to avoid further confusion.
Beth Kieler
SourceGear Technical Support
Hi Beth,
Thanks a ton! Escaping the $ did the trick! Again thanks!
My Git installation folder has both git-bash.exe and git-cmd.exe and the Git installer creates a shortcut that points to git-bash.exe - yes, so I am using git-bash.exe and msysgit (not, MySysGit - probably it was your typo)
For what conditions or reason should I use git-cmd.exe?
Can you give simple explanation of the variables $LOCAL, $REMOTE, $BASE, $MERGED? I got some explanation but I am very clear about them (talks about diff-pre-image e.t.c) OR you can point to me any doc that gives a lucid explanation!
PS: The DiffMerge documentation's confusing guidelines was the source of problem - and another thing - the documentation "code"s should not have line breaks - that's awful for users! We can't copy as it is!
Q1: Unfortunately, I don't really know. You'll have to ask the makers of Git.
Q2: $Local is usually the file version that is in your current working area. $Remote is usually the file version that is in your source control system. $Base is the baseline or common ancestor of both files. $Merged is the result of merging $Local and $Remote.
Beth Kieler
SourceGear Technical Support
14 posts • Page 1 of 1
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South Plainfield, NJ - March 25, 2011 -- Petra Solar, a pioneer and market leader in smart solar technology for utility companies that combines distributed solar energy generation with building a Smart Grid infrastructure, announced today the appointment of Dan Brdar as Chief Operating Officer. Mr. Brdar will assume this vital role with responsibility for the strategic and operational leadership of the company's sales, marketing, operations, and engineering organizations.
"I am delighted to have Dan join the Petra Solar executive leadership team in the critical role of Chief Operating Officer," said Petra Solar President and CEO, Dr. Shihab Kuran. "Petra Solar's innovative SunWaveT system provides our utility partners with a powerful platform that transforms the way solar power is produced and delivered. I have no doubt that Dan's extensive expertise, strategic vision and proven leadership will help Petra Solar continue our positive momentum and business performance, capitalize on the enormous growth opportunities that exist in today's global market, and set a trajectory toward even greater levels of success for the company. "
Mr. Brdar brings with him over 30 years of combined technology development, new product introduction and sales leadership experience in a variety of executive positions. Prior to joining Petra Solar, he served as President, Chief Executive Officer and Chairman of the Board of FuelCell Energy, the world's leading stationary fuel cell manufacturer with five facilities for production and service located in three countries. At FuelCell, Mr. Brdar led the growth strategies, financial planning and capital creation efforts, new product and market development initiatives, and provided strategic direction to manufacturing, engineering and service operations. While there, Mr. Brdar was responsible for raising over $100 million in corporate funds from institutional investors and partners, converting negative product gross margins to positive via a 51% improvement, leading a 220% increase in the manufacturing production rate, and driving a record sales order backlog.
Before joining FuelCell Energy, Mr. Brdar held management positions at General Electric where he focused on new product introduction programs for the GE Power Systems business unit and managed its gas turbine product lines, which generated multi-billion dollar annual new unit sales. Prior to GE, he was Associate Director, Office of Power Systems Product Management, at the U.S. Department of Energy where he was responsible for directing the research, development and demonstration of advanced power systems including advanced gas turbines, gasification systems and fuel cells. He earned his Bachelor of Science Degree in Engineering from the University of Pittsburgh in 1981.
"When you look at the incredible portfolio of solar and Smart Grid products and technologies Petra Solar is poised to deliver, I see great opportunity in the markets in which it currently serves, as well as those where we will expand," said Mr. Brdar. "With the world in the midst of a clean energy revolution, Petra Solar's suite of products and services provides utilities around the globe with reliable, cost effective solutions that can assist them in preparing the electric grid to meet the energy needs of the 21st century. I am thrilled to join an organization that is so passionate about confronting today's renewable energy challenges with innovative advancements that address the growing global demand for sustainable energy and grid reliability."
About Petra Solar:
About Petra Solar:
Petra Solar, founded in 2006 by CEO and President Dr. Kuran, is the pioneer of SunWaveT, a new technology that combines distributed solar energy generation with Smart Grid communications and improved grid reliability features to create a comprehensive utility grade solution. One of the key advantages of the Petra Solar solution is its flexible grid integration architecture. Petra Solar is the only cleantech company that provides utility-grade, grid-tied, distributed smart solar systems that can be installed on existing assets such as utility and streetlight poles. Petra Solar's success is the culmination of more than 18 years of research and development. For more information about Petra Solar visit www.petrasolar.com.
Mary Grikas
Vice President Communications, Petra Solar
Phone: 732-429-3908
E-mail: [email protected]