Recording advances for neural prosthetics

An important challenge for neural prosthetics research is to record from populations of neurons over long periods of time, ideally for the lifetime of the patient. Two new advances toward this goal are described, the use of local field potentials (LFPs) and autonomously positioned recording electrodes. LFPs are the composite extracellular potential field from several hundreds of neurons around the electrode tip. LFP recordings can be maintained for longer periods of time than single cell recordings. We find that similar information can be decoded from LFP and spike recordings, with better performance for state decodes with LFPs and, depending on the area, equivalent or slightly less than equivalent performance for signaling the direction of planned movements. Movable electrodes in microdrives can be adjusted in the tissue to optimize recordings, but their movements must be automated to be a practical benefit to patients. We have developed automation algorithms and a meso-scale autonomous electrode testbed, and demonstrated that this system can autonomously isolate and maintain the recorded signal quality of single cells in the cortex of awake, behaving monkeys. These two advances show promise for developing very long term recording for neural prosthetic applications

Parameterized Edge Hamiltonicity

We study the parameterized complexity of the classical Edge Hamiltonian Path problem and give several fixed-parameter tractability results. First, we settle an open question of Demaine et al. by showing that Edge Hamiltonian Path is FPT parameterized by vertex cover, and that it also admits a cubic kernel. We then show fixed-parameter tractability even for a generalization of the problem to arbitrary hypergraphs, parameterized by the size of a (supplied) hitting set. We also consider the problem parameterized by treewidth or clique-width. Surprisingly, we show that the problem is FPT for both of these standard parameters, in contrast to its vertex version, which is W-hard for clique-width. Our technique, which may be of independent interest, relies on a structural characterization of clique-width in terms of treewidth and complete bipartite subgraphs due to Gurski and Wanke

Linear-time protein 3-D structure searching with insertions and deletions

<p>Abstract</p> <p>Background</p> <p>Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools for searching for similar structures in biomolecular 3-D structure databases are becoming increasingly important in the structural biology of the post-genomic era.</p> <p>Results</p> <p>We consider an important, fundamental problem of reporting all substructures in a 3-D structure database of chain molecules (such as proteins) which are similar to a given query 3-D structure, with consideration of indels (<it>i.e.</it>, insertions and deletions). This problem has been believed to be very difficult but its exact computational complexity has not been known. In this paper, we first prove that the problem in unbounded dimensions is NP-hard. We then propose a new algorithm that dramatically improves the average-case time complexity of the problem in 3-D in case the number of indels <it>k </it>is bounded by a constant. Our algorithm solves the above problem for a query of size <it>m </it>and a database of size <it>N </it>in average-case <it>O</it>(<it>N</it>) time, whereas the time complexity of the previously best algorithm was <it>O</it>(<it>Nm</it>^<it>k</it>+1).</p> <p>Conclusions</p> <p>Our results show that although the problem of searching for similar structures in a database based on the RMSD measure with indels is NP-hard in the case of unbounded dimensions, it can be solved in 3-D by a simple average-case linear time algorithm when the number of indels is bounded by a constant.</p

A consensus guide to capturing the ability to inhibit actions and impulsive behaviors in the stop-signal task

© Verbruggen et al. Response inhibition is essential for navigating everyday life. Its derailment is considered integral to numerous neurological and psychiatric disorders, and more generally, to a wide range of behavioral and health problems. Response-inhibition efficiency furthermore correlates with treatment outcome in some of these conditions. The stop-signal task is an essential tool to determine how quickly response inhibition is implemented. Despite its apparent simplicity, there are many features (ranging from task design to data analysis) that vary across studies in ways that can easily compromise the validity of the obtained results. Our goal is to facilitate a more accurate use of the stop-signal task. To this end, we provide 12 easy-to-implement consensus recommendations and point out the problems that can arise when they are not followed. Furthermore, we provide user-friendly open-source resources intended to inform statistical-power considerations, facilitate the correct implementation of the task, and assist in proper data analysis

Clique-width : harnessing the power of atoms.

Many NP-complete graph problems are polynomial-time solvable on graph classes of bounded clique-width. Several of these problems are polynomial-time solvable on a hereditary graph class G if they are so on the atoms (graphs with no clique cut-set) of G . Hence, we initiate a systematic study into boundedness of clique-width of atoms of hereditary graph classes. A graph G is H-free if H is not an induced subgraph of G, and it is (H1,H2) -free if it is both H1 -free and H2 -free. A class of H-free graphs has bounded clique-width if and only if its atoms have this property. This is no longer true for (H1,H2) -free graphs, as evidenced by one known example. We prove the existence of another such pair (H1,H2) and classify the boundedness of clique-width on (H1,H2) -free atoms for all but 18 cases

How much choice is there in housing choice vouchers? Neighborhood risk and free market rental housing accessibility for active drug users in Hartford, Connecticut

<p>Abstract</p> <p>Background</p> <p>Since the mid-1970s, the dominant model for U.S. federal housing policy has shifted from unit-based programs to tenant based vouchers and certificates, intended to allow recipients a choice in their housing and neighborhoods. Surprisingly little research has examined the question of where those with Section 8 housing vouchers are able to live, but some research suggests that voucher holders are more likely to reside in distressed neighborhoods than unsubsidized renter households. Further, federal housing policy has limited drug users' access to housing subsidies. In turn, neighborhood disorder has been associated with higher levels of injection drug risk behaviors, and higher drug-related mortality. This paper explores rental accessibility and neighborhood characteristics of advertised rental housing in Hartford CT.</p> <p>Methods</p> <p>Brief telephone interviews were conducted with landlords or management companies with units to rent in Hartford to explore housing accessibility measured as initial move in costs, credit and criminal background checks, and whether rental subsidies were accepted. These data were supplemented with in-depth interviews with landlords, shelter staff and active users of heroin, crack or cocaine. Apartments for rent were geocoded and mapped using <b>ArcGIS</b>. We used location quotients to identify areas where low-income rental housing is concentrated. Finally, we mapped apartments in relation to drug and violent arrest rates in each neighborhood.</p> <p>Results</p> <p>High security deposits, criminal background and credit checks limit housing accessibility even for drug users receiving vouchers. While most landlords or management companies accepted housing subsidies, several did not. Voucher units are concentrated in neighborhoods with high poverty neighborhoods. Landlords reported little incentive to accept rental subsidies in neighborhoods with low crime rates, but appreciated the guarantee provided by Section 8 in high crime neighborhoods that were less likely to attract applicants with good jobs and credit.</p> <p>Conclusion</p> <p>Housing vouchers in themselves do not greatly improve recipients' choice of neighborhood and voucher units are concentrated in the most distressed neighborhoods. Policy changes are needed to increase landlords' incentives to accept housing subsidies. Interventions to improve neighborhood conditions are needed to improve the probability of success for those recovering from drug addictions.</p