Polyhedral computational geometry for averaging metric phylogenetic trees

This paper investigates the computational geometry relevant to calculations of the Frechet mean and variance for probability distributions on the phylogenetic tree space of Billera, Holmes and Vogtmann, using the theory of probability measures on spaces of nonpositive curvature developed by Sturm. We show that the combinatorics of geodesics with a specified fixed endpoint in tree space are determined by the location of the varying endpoint in a certain polyhedral subdivision of tree space. The variance function associated to a finite subset of tree space has a fixed $C^\infty$ algebraic formula within each cell of the corresponding subdivision, and is continuously differentiable in the interior of each orthant of tree space. We use this subdivision to establish two iterative methods for producing sequences that converge to the Frechet mean: one based on Sturm's Law of Large Numbers, and another based on descent algorithms for finding optima of smooth functions on convex polyhedra. We present properties and biological applications of Frechet means and extend our main results to more general globally nonpositively curved spaces composed of Euclidean orthants.Comment: 43 pages, 6 figures; v2: fixed typos, shortened Sections 1 and 5, added counter example for polyhedrality of vistal subdivision in general CAT(0) cubical complexes; v1: 43 pages, 5 figure

Age-related differentiation of sensorimotor control strategies during pursuit and compensatory tracking

Motor control deficits during aging have been well-documented. Various causes of neuromotor decline, including both peripheral and central neurological deficits, have been hypothesized. Here, we use a model of closed-loop sensorimotor control to examine the functional causes of motor control deficits during aging. We recruited 14 subjects aged 19-61 years old to participate in a study in which they performed single-joint compensatory and pursuit tracking tasks with their dominant hand. We found that visual response delay and visual noise increased with age, while reliance on visual feedback, especially during compensatory tracking decreased. Increases in visual noise were also positively correlated with increases in movement error during a reach and hold task. The results suggest an increase in noise within the visuomotor control system may contribute to the decline in motor performance during early aging

Visual and Proprioceptive Contributions to Compensatory and Pursuit Tracking Movements in Humans

An ongoing debate in the field of motor control considers how the brain uses sensory information to guide the formation of motor commands to regulate movement accuracy. Recent research has shown that the brain may use visual and proprioceptive information differently for stabilization of limb posture (compensatory movements) and for controlling goal-directed limb trajectory (pursuit movements). Using a series of five experiments and linear systems identification techniques, we modeled and estimated the sensorimotor control parameters that characterize the human motor response to kinematic performance errors during continuous compensatory and pursuit tracking tasks. Our findings further support the idea that pursuit and compensatory movements of the limbs are differentially controlled

Evolution of the mysRS element in the genome of rodent species

Retrotransposons are a type of transposable element in which DNA copies are produced via an RNA intermediate and integrate into new chromosomal sites continually contributing to the dynamics of genomes. While sequencing the mys element among the Cricetidae family of rodents, we identified a previously uncharacterized element in the genome of the Mexican volcano mouse that we refer to as mys-related sequence (mysRS). This investigation provides a unique opportunity to contrast the evolution of the two retrotransposon families apparently restricted to a specific taxonomic group of rodents. By analyzing the genomes of various cricetid rodents, our results provide evidence that the mysRS element originated in either an ancestor of the Neotominae subfamily or the Reithrodontomini tribe of rodents, which diverged roughly nine million years ago, and predates the appearance of the mys element

Junior Faculty Engagement at iSchools: Personal Experience during the First Several Years

This roundtable discussion will explore how junior faculty at iSchools have been able to embed their research, teaching, and service activities within their schools, the larger institutions, and broader communities. The session will also focus on the ways in which junior faculty have received guidance in their roles--from the job search through the first several years in a tenure-track position. Roundtable leaders represent a variety of institutions and experiences--as faculty at the University of Illinois at Urbana-Champaign [WJM], the University of Maryland [SP], the University of North Carolina at Chapel Hill [PME], and the University of Texas at Austin [MW], and with doctoral-level preparation at the University of North Carolina at Chapel Hill [WJM, MW], the University of Toronto [SP], and the University of Washington [PME]. While the annual junior faculty mentoring event at the iConference specifically targets junior faculty as participants, this roundtable session offers a more inclusive environment for the discussion of this topic, specifically engaging doctoral students and senior faculty as well as their junior colleagues

Intention Tremor and Deficits of Sensory Feedback Control in Multiple Sclerosis: a Pilot Study

Background Intention tremor and dysmetria are leading causes of upper extremity disability in Multiple Sclerosis (MS). The development of effective therapies to reduce tremor and dysmetria is hampered by insufficient understanding of how the distributed, multi-focal lesions associated with MS impact sensorimotor control in the brain. Here we describe a systems-level approach to characterizing sensorimotor control and use this approach to examine how sensory and motor processes are differentially impacted by MS. Methods Eight subjects with MS and eight age- and gender-matched healthy control subjects performed visually-guided flexion/extension tasks about the elbow to characterize a sensory feedback control model that includes three sensory feedback pathways (one for vision, another for proprioception and a third providing an internal prediction of the sensory consequences of action). The model allows us to characterize impairments in sensory feedback control that contributed to each MS subject’s tremor. Results Models derived from MS subject performance differed from those obtained for control subjects in two ways. First, subjects with MS exhibited markedly increased visual feedback delays, which were uncompensated by internal adaptive mechanisms; stabilization performance in individuals with the longest delays differed most from control subject performance. Second, subjects with MS exhibited misestimates of arm dynamics in a way that was correlated with tremor power. Subject-specific models accurately predicted kinematic performance in a reach and hold task for neurologically-intact control subjects while simulated performance of MS patients had shorter movement intervals and larger endpoint errors than actual subject responses. This difference between simulated and actual performance is consistent with a strategic compensatory trade-off of movement speed for endpoint accuracy. Conclusions Our results suggest that tremor and dysmetria may be caused by limitations in the brain’s ability to adapt sensory feedback mechanisms to compensate for increases in visual information processing time, as well as by errors in compensatory adaptations of internal estimates of arm dynamics

Hitchhiking and Recombination in Birds: Evidence from Mhc-linked and Unlinked Loci in Red-winged Blackbirds (Agelaius phoeniceus)

Hitchhiking phenomena and genetic recombination have important consequences for a variety of fields for which birds are model species, yet we know virtually nothing about naturally occurring rates of recombination or the extent of linkage disequilibrium in birds. We took advantage of a previously sequenced cosmid clone from Red-winged Blackbirds (Agelaius phoeniceus) bearing a highly polymorphic Mhc class II gene, Agph-DABI, to measure the extent of linkage disequilibrium across similar to40 kb of genomic DNA and to determine whether non-coding nucleotide diversity was elevated as a result of physical proximity to a target of balancing. selection. Application of coalescent theory predicts that the hitchhiking effect is enhanced by the larger effective population size of blackbirds compared with humans, despite the presumably higher rates of recombination in birds. We surveyed sequence polymorphism at three Mhc-linked loci occurring 1.5-40 kb away from Agph-DABI and found that nucleotide diversity was indistinguishable from that found at three presumably unlinked, non-coding introns (beta-actin intron 2, beta-fibrinogen intron 7 and rhodopsin intron 2). Linkage disequilibrium as measured by Lewontin's D' was found only across a few hundred base pairs within any given locus, and was not detectable among any Mhc-linked loci. Estimated rates of the per site recombination rate p derived from three different analytical methods suggest that the amounts of recombination in blackbirds are up to two orders of magnitude higher than in humans, a discrepancy that cannot be explained entirely by the higher effective population size of blackbirds relative to humans. In addition, the ratio of the number of estimated recombination events per mutation frequently exceeds 1, as in Drosophila, again much higher than estimates in humans. Although the confidence limits of the blackbird estimates themselves span an order of magnitude, these data suggest that in blackbirds the hitchhiking effect for this region is negligible and may imply that the per site per individual recombination rate is high, resembling those of Drosophila more than those of humans.Organismic and Evolutionary Biolog

Examining the Roles of the Conserved mRNA Deadenylase Complex on Drosophila Neuronal Structures

The most common cause of inherited mental deficiency and monogenetic cause of autism is Fragile X Syndrome (FXS). There is little known about the origins of this disease which will be investigated in the present study. The series of experiments conducted examined the potential role of mRNA deadenylation proteins as contributing factors to the pathogenesis of FXS using Drosophila melanogaster as a model organism. One of the main complexes involved in deadenylation is the CNOT complex, which is comprised of many proteins, including POP2, TWIN, and NOT3. Each protein plays a unique role within the CNOT complex. This goal of this study was to further characterize these genes. Previous research in the Barbee lab has shown that these genes influence synapse development of the pre-synaptic terminal at the larval neuromuscular junction in D. melanogaster. However, it had not been tested whether POP2, TWIN, and NOT3 also have a post-synaptic effect. The localization of these genes at the neuromuscular junction was also examined and they were found to be concentrated in the pre-synaptic terminal. Finally, this study looked at whether these genes had any role in the development of sensory neurons. There was a significant increase in sensory neuron dendritic growth and a significant decrease in the complexity of the dendritic branches. These results provide insight into the characterization of TWIN, POP2, and NOT3, and their roles within the development of D. melanogaster. Future experiments will examine the genetic and biochemical relationship between the deadenylase complex and FXS in the D. melanogaster model