Doctoral Dissertation

My dissertation, entitled “Comparative topological analysis of neuronal arbors via sequence representation and alignment”, is focused on applying bioinformatic approaches to neuronal morphology to enable new discoveries and increase understanding about how morphology and neuron function interrelate.

Recycle your plastic gift and credit cards

Between gifts cards, credit cards, and old health insurance cards, I’ve got a far bit of plastic in my drawer. It finally dawned on me to just look it up online, and lo and behold, someone is recycling them. Earthworks System, LLC takes the cards, grinds them up, and then creates new PVC sheets (that’s what they’re made of) so new cards can be made.

Send your cards to

Earthworks System, LLC
33200 Bainbridge Road, Suite E
Solon, OH 44139

Based on “Can I recycle plastic gift cards?” at Mother Nature Network.


Caution when consuming media

On The Media released a handbook for how to treat media reports, particularly during and immediately following a major event. The release was last year, but the information is just as important today and in the future. Point 9 is quite important, but I think could go further. You are part of the social media and are responsible for what you post. Take care when linking to or quoting an article. When you post to something that turns out to be wrong, your credibility is harmed. If you are unsure of a report but feel it is worth posting, say so explicitly. Good communication is everything.

Fed whistleblower and regulatory capture (Story in BoingBoing)

The story: Fed whistleblower secretly recorded 46 hours of regulatory capture inside Goldman Sachs

From the piece:

The Fed had vowed to reform this culture, and Segarra was supposed to be part of that mission. But once she reported for work at the Fed department at Goldman Sachs (Fed regulators actually work at desks inside the banks they’re regulating), she discovered a culture rotten with cowardice and capture, where her boss’s idea of a really stern rebuke for lying in official filings was to mildly mention that there appeared to be some irregularities in the compliance regime, then trailing off ineffectually.

We know this because of the recordings, which were edited into a documentary by This American Life that aired yesterday. It’s an absolutely riveting and essential hour of audio (MP3), and the accompanying package by Pro Publica is likewise essential reading.

Congress and/or President Obama could do something about this, not overnight, but given some prioritization. The problem of course is that they are bought as well. Some folks need to go to jail, but in any case we need electoral reform so that we can actually have a government willing to take on this sort of corruption.

Qualcomm’s Neuromorphic Endeavors

IBM may have been the first to release a neuromorphic chip, but Qualcomm is hot on their heals. The release date isn’t yet set (or at least it isn’t known), however according to MIT Technology Review, “the company will spend 2014 signing up researchers to try out the technology.” The effort is called the Zeroth Program, based on the later added “Zeroth” law of Asimov’s laws of robotics. The name seems more a nod than anything to do with the chip itself since the field is still too primitive to be dealing with laws of motivation and behavior, however another entry into the field should be greatly welcomed. Much is yet to be determined with regards to the synaptic integration, plasticity, and connectivity parameters required for particular functions and levels of performance in a robot imbued with intelligence via neuromorphic chip.

A demo this past spring, reported in several articles, displayed a robot cleaning up toys given only instructions via the body language of an engineer. Existing robots can do such a task, so time and further testing will tell …

IBM’s TrueNorth – The first neuromorphic chip

IBM has recently released details of a neuromorphic chip named TrueNorth via their website, the press, and a research report in the journal Science. The research team, headed by Dharmendra Modha as part of the DARPA SyNAPSE Program, developed a chip containing a million “programmable spiking neurons” and 256 million synapses. The chips use 5.4 billion transistors on 4096 “neurosynaptic cores” which each has its memory (in the form of connection routing and timing delays) close to its “neuronal” processing units.

The United States is an Oligarchy

A group at Princeton recently completed a study (to be published this Fall of 2014) that shows pretty definitively that over the 80’s and 90’s (the period studied), the United States government has represented wealthy interests and ignored the broader public interest.

The study is entitled Testing Theories of American Politics: Elites, Interest Groups, and Average Citizens (see original pdf preprint), and it looks at the correlations between policy preferences of particular groups and policy outcomes. The authors looked at preferences of wealthy citizens, average citizens, wealthy/commercial organizations, and public organizations without a commercial interest. While often it appears that the federal government is acting on behalf of the people, the data and analysis strongly suggest that is only because of how often the preferences of the average citizen aligns with the preferences of the wealthy interests.

This story was covered by multiple sources back in April. Here’s an article at the BBC. It was also covered by The Young Turks, an online news network that has spent a large amount of time on the issue of corruption and money in politics:

How does a cat land on its feet?

A perfect example of science and fun! Ever wonder how a cat is able to flip over so quickly and ensure it lands on its feet? Some super slow-motion capture and some careful handling of cats (none harmed in the making of the video) provides a look:

Wolf PAC Petition Calling for a Constitutional Amendment

We have a problem of corruption here in the United States (see other posts in this section) with multiple causes and manifestations. Money in politics is one major driver, which over our history has led to greater concentration of power which has in turn made money in politics an even bigger problem. Two-party politics, public apathy, and gerrymandering all play a role as well. Many groups are attempting to address it. Several organizations are taking on the problem, including the Mayday PAC (led by Lawrence Lessig), Public Citizen, Move to Amend, Represent.Us, and Wolf PAC, among others. The following is a brief overview connecting the dots to a call for an Article V convention (made possible by the US Constitution).

Particularly in Congress/at the federal level, money has massively corrupted our government such that just about every issue you might care about is dominated by not just special interests, but moneyed corporate interests. Representatives spend more than half their time raising money rather than dealing with the issues (whether that be spending time with other reps, studying the issues, or hearing from constituents). While an increase in voter participation would be a huge help, the money will continue to flow and …

Mining Tree Patterns Poster

PDF of Poster

Neuronal morphology plays a major role in the electrophysiological and connectivity characteristics of neurons, and thus in neuron and network function.

Various morphometrics have been applied in studying neurons; however, the structural patterns of the tree-like dendrites and axons have yet to be fully explored. These patterns may reflect strategies that achieve functional properties such as dendritic compartmentalization, space filling, and targeting of various spatial distributions of synapses.

To address these issues we analyzed thousands of neurons, made available via NeuroMorpho.Org, in terms of structural patterns by representing their arbors (axons, dendrites, apical dendrites) as gene-like sequences. We compared neurons by arborization type within and between cell classes using sequence analysis techniques. Sequence domains can be used in conjunction with functional studies to further elucidate the structure-function relationship.

Neuronal Morphology Background

Morphology is the study of the physical shape of things for the purposes of understanding the processes involved in forming an object and/or the purpose/function of the object. We know that neurons are involved in converting environmental stimuli into electrochemical signals, processing that information, producing consciousness, and enabling behavior. Through studies of morphology, often in conjunction with electrophysiology, gene and protein expression, and other properties of neurons, neuroscientists have learned much about what specifically neurons do and how their various individual functions contribute to more emergent phenomena vital to brain function. The first chapter of my dissertation (and the book chapter “Measuring and Modeling Morphology: How Dendrites Take Shape“, of Springer textbook Computational Systems Neurobiology) discusses many of the relationships between morphology, function, and other neuronal properties, along with the major approaches (old and new) used in making the discoveries.

After discussing the relevance of morphology in neuroscience, the chapter begins with an description of morphological metrics and the relationships between morphological and electrophysiological features. An review of molecular pathways involved in neuronal development and plasticity follows. Having provided the context of molecular pathways and electrophysiological function, the chapter describes a diverse set of studies using simulations at various levels of …


Gillette TA, Ascoli GA (2015) Topological characterization of neuronal arbor morphology via sequence representation: I – Motif analysis. BMC Bioinformatics, 16.
Summary | PDF

Gillette TA, Hosseini P, Ascoli GA (2015) Topological characterization of neuronal arbor morphology via sequence representation: II – Global alignmentBMC Bioinformatics, 16.
Summary | PDF

Polavaram S, Gillette TA, Parekh R, Ascoli GA (2014) Statistical analysis and data mining of digital reconstructions of dendritic morphologies. Frontiers in Neuroanatomy, 8:138.

Gillette TA, Brown KM, Ascoli GA (2011) The DIADEM Metric: Comparing multiple reconstructions of the same neuronNeuroinformatics, 9:233-45.

Gillette TA, Brown KM, Svoboda K, Liu Y, Ascoli GA (2011) DIADEMchallenge.Org: A compendium of resources fostering the contiuous development of automated neuronal reconstruction. Neuroinformatics, 9:2-3.

Gillette TA, Ascoli GA. Measuring and Modeling Morphology: How Dendrites Take Shape. In Le Novere N. (Ed.), “Computational Systems Neurobiology”, pp. 387-428, Springer (2012).

Theodore C Dumas, Todd A Gillette, Deveroux Ferguson et al. (2010) Anti-glucocorticoid gene therapy reverses the impairing effects of elevated corticosterone on spatial memory, hippocampal neuronal excitability, …

Cleaning Up a Broken Compact Fluorescent Lightbulb (CFL)

Twice in one week to people I know? Yep, it’s time for a PSA. No need to freak out, but that powdery stuff in compact fluorescent light bulbs IS hazardous (it contains mercury).

Here’s the EPA’s how-to:

(originally shared via Google+ on May 21, 2014)

Analyzing Neuronal Morphology with Gene Sequencing Approaches

Analysis of neuronal morphology has until recently been limited to small data sets due to the amount of time necessary to generate a digitized representation of a neuron’s structure.

Recent efforts to curate data from many different labs working in parallel on vastly differing topics has led to the NeuroMorpho.Org database which currently provides access and metadata for over 10,000 neurons from a variety of species, cell types, brain regions, and experimental conditions.

Quantitative Measuring of Neuronal Reconstructions – The DIADEM Metric

Summary: This post summarizes some recent efforts in the fields of neuroscience and computer vision to improve neuronal reconstructions, particularly the DIADEM metric, a measure used to evaluate reconstructions produced by algorithms.


Gillette TA, Brown KM, Ascoli GA. The DIADEM Metric: Comparing multiple reconstructions of the same neuron. Neuroinformatics, 9:233-245 (2011).

Gillette TA, Brown KM, Svoboda K, Liu Y, Ascoli GA. DIADEMchallenge.Org: A Compendium of Resources Fostering the Continuous Development of Automated Neuronal Reconstruction. Neuroinformatics, 9:303–304 (2011).

Almost all fields, particularly in biology, are greatly benefited by having a large data set. Morphological reconstructions of neurons obviously benefit the study of neuronal morphology, but also the related fields of neuron growth, neuron function with regards to drug and/or dysfunction, connectomics, among many others. Until recently reconstructions were generated and analyzed for a particular study, occasionally being reused when another lab requested it or for a follow-up study. NeuroMorpho.Org helped to change this by bringing together reconstructions from labs around the world doing a variety of experiments. Now will over 10,000 reconstructions there are many questions that can be asked that could not be before so many were brought together.

Nonetheless, 10,000 is not so many when one considers the vast diversity of …

Presentation of Integrated Information Theory at Mind Guild July 8, 2014

The monthly Mind Guild will meet again Tuesday July 8th in the Conference Room (222) of the Krasnow Institute for Advanced Study. In the next several meetings the Guild will attempt to cover several of the current approaches to understanding consciousness and dealing with the “hard problem” as described by philosopher David Chalmers. Chalmers’ own views will be covered in a later meeting, however the upcoming meeting will focus on two perspectives on Integrated Information Theory (IIT).

Initially proposed by Giulio Tononi of the University of Wisconsin, IIT has reached its 3rd iteration. The core underlying idea is that subjective experience is intrinsic to information, and that consciousness experience can be defined as the irreducible integrated information of a network. Physicist Max Tegmark took expanded upon the idea to explore IIT with regards to physical systems generally in the paper “Consciousness as a State of Matter” (see a video of Tegmark lecturing about his recent paper). In the meeting this concepts will be explained and explored in greater detail.

Previous topics covered in the Mind Guild have included philosopher John Searle’s views, the thalamocortical loop theory …

Anti-glucocorticoid Gene Therapy Reverses the Impairing Effects of Elevated Corticosterone

Full Title: Anti-glucocorticoid gene therapy reverses the impairing effects of elevated corticosterone on spatial memory, hippocampal neuronal excitability, and synaptic plasticity


Moderate release of the major stress hormones, glucocorticoids (GCs), improves hippocampal function and memory. In contrast, excessive or prolonged elevations produce impairments. Enzymatic degradation and reformation of GCs help to maintain optimal levels within target tissues, including the brain. We hypothesized that expressing a GC-degrading enzyme in hippocampal neurons would attenuate the negative impact of an excessive elevation in GC levels on synaptic physiology and spatial memory. We tested this by expressing 11-beta-hydroxysteroid dehydrogenase (type II) in dentate gyrus granule cells during a 3 d GC treatment followed by examination of synaptic responses in hippocampal slices or spatial performance in the Morris water maze. In adrenalectomized rats with basal GC replacement, additional GC treatments for 3 d reduced synaptic strength and promoted the expression of long-term depression at medial perforant path synapses, increased granule cell and CA1 pyramidal cell excitability, and impaired spatial reference memory (without influencing learning). Expression of 11-beta-hydroxysteroid dehydrogenase (type II), mostly in mature dentate gyrus granule cells, reversed the effects of high GC levels on granule cell and pyramidal cell excitability, perforant path synaptic plasticity, …

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