Neural Shrubs: Using Neural Networks to Improve Decision Trees

Decision trees are a method commonly used in machine learning to either predict a categorical response or a continuous response variable. Once the tree partitions the space, the response is either determined by the majority vote – classification trees, or by averaging the response values – regression trees. This research builds a standard regression tree and then instead of averaging the responses, we train a neural network to determine the response value. We have found that our approach typically increases the predicative capability of the decision tree. We have 2 demonstrations of this approach that we wish to present as a poster at the SDSU Data Symposium

Rapid inversion: running animals and robots swing like a pendulum under ledges.

Escaping from predators often demands that animals rapidly negotiate complex environments. The smallest animals attain relatively fast speeds with high frequency leg cycling, wing flapping or body undulations, but absolute speeds are slow compared to larger animals. Instead, small animals benefit from the advantages of enhanced maneuverability in part due to scaling. Here, we report a novel behavior in small, legged runners that may facilitate their escape by disappearance from predators. We video recorded cockroaches and geckos rapidly running up an incline toward a ledge, digitized their motion and created a simple model to generalize the behavior. Both species ran rapidly at 12-15 body lengths-per-second toward the ledge without braking, dove off the ledge, attached their feet by claws like a grappling hook, and used a pendulum-like motion that can exceed one meter-per-second to swing around to an inverted position under the ledge, out of sight. We discovered geckos in Southeast Asia can execute this escape behavior in the field. Quantification of these acrobatic behaviors provides biological inspiration toward the design of small, highly mobile search-and-rescue robots that can assist us during natural and human-made disasters. We report the first steps toward this new capability in a small, hexapedal robot

Facilitating Constructive Discussions of Difficult Socio-Scientific Issues

Discussion can be an important and powerful tool in efforts to build a more diverse, equitable, and inclusive future for STEM (i.e., science, technology, engineering, and mathematics). However, facilitating discussions on difficult, complex, and often uncomfortable issues, like racism and sexism, can feel daunting. We outline a series of steps that can be used by educators to facilitate productive discussions that empower everyone to listen, contribute, learn, and ultimately act to transform STEM

Live Coding, Live Notation, Live Performance

This paper/demonstration explores relationships between code, notation including representation, visualisation and performance. Performative aspects of live coding activities are increasingly being investigated as the live coding movement continues to grow and develop. Although live instrumental performance is sometimes included as an accompaniment to live coding, it is often not a fully integrated part of the performance, relying on improvisation and/or basic indicative forms of notation with varying levels of sophistication and universality. Technologies are developing which enable the use of fully explicit music notations as well as more graphic ones, allowing more fully integrated systems of code in and as performance which can also include notations of arbitrary complexity. This itself allows the full skills of instrumental musicians to be utilised and synchronised in the process. This presentation/demonstration presents work and performances already undertaken with these technologies, including technologies for body sensing and data acquisition in the translation of the movements of dancers and musicians into synchronously performable notation, integrated by live and prepared coding. The author together with clarinetist Ian Mitchell present a short live performance utilising these techniques, discuss methods for the dissemination and interpretation of live generated notations and investigate how they take advantage of instrumental musicians’ training-related neuroplasticity skills

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

We describe a strategy for constructing atomic resolution dynamical ensembles of RNA molecules, spanning up to millisecond timescales, that combines molecular dynamics (MD) simulations with NMR residual dipolar couplings (RDC) measured in elongated RNA. The ensembles are generated via a Monte Carlo procedure by selecting snap-shot from an MD trajectory that reproduce experimentally measured RDCs. Using this approach, we construct ensembles for two variants of the transactivation response element (TAR) containing three (HIV-1) and two (HIV-2) nucleotide bulges. The HIV-1 TAR ensemble reveals significant mobility in bulge residues C24 and U25 and to a lesser extent U23 and neighboring helical residue A22 that give rise to large amplitude spatially correlated twisting and bending helical motions. Omission of bulge residue C24 in HIV-2 TAR leads to a significant reduction in both the local mobility in and around the bulge and amplitude of inter-helical bending motions. In contrast, twisting motions of the helices remain comparable in amplitude to HIV-1 TAR and spatial correlations between them increase significantly. Comparison of the HIV-1 TAR dynamical ensemble and ligand bound TAR conformations reveals that several features of the binding pocket and global conformation are dynamically preformed, providing support for adaptive recognition via a ‘conformational selection’ type mechanism

FRET studies of a landscape of Lac repressor-mediated DNA loops

DNA looping mediated by the Lac repressor is an archetypal test case for modeling protein and DNA flexibility. Understanding looping is fundamental to quantitative descriptions of gene expression. Systematic analysis of LacI•DNA looping was carried out using a landscape of DNA constructs with lac operators bracketing an A-tract bend, produced by varying helical phasings between operators and the bend. Fluorophores positioned on either side of both operators allowed direct Förster resonance energy transfer (FRET) detection of parallel (P1) and antiparallel (A1, A2) DNA looping topologies anchored by V-shaped LacI. Combining fluorophore position variant landscapes allows calculation of the P1, A1 and A2 populations from FRET efficiencies and also reveals extended low-FRET loops proposed to form via LacI opening. The addition of isopropyl-β-d-thio-galactoside (IPTG) destabilizes but does not eliminate the loops, and IPTG does not redistribute loops among high-FRET topologies. In some cases, subsequent addition of excess LacI does not reduce FRET further, suggesting that IPTG stabilizes extended or other low-FRET loops. The data align well with rod mechanics models for the energetics of DNA looping topologies. At the peaks of the predicted energy landscape for V-shaped loops, the proposed extended loops are more stable and are observed instead, showing that future models must consider protein flexibility

A Guide to Conscious Editing at Wilson Special Collections Library

This is the final version of The Guide to Conscious Editing for Wilson Special Collections Library. The work was created by the Conscious Editing Steering Committee for the University Libraries of the University of North Carolina at Chapel Hill. Between September 2019 and April 2022, more than twenty archivists, librarians, and humanities scholars contributed to the Guide