Digital Commons Network^™

Review Paper: The Shape Of Phylogenetic Treespace, Katherine St. John

Publications and Research

Trees are a canonical structure for representing evolutionary histories. Many popular criteria used to infer optimal trees are computationally hard, and the number of possible tree shapes grows super-exponentially in the number of taxa. The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and in running time, and the analysis and visualization of results. We review the past work on analyzing and comparing trees by their shape as well as recent work that incorporates trees with weighted branch lengths.

Associated Production Of A Top Pair And A Higgs Boson Beyond Nlo, Alessandro Broggio, Andrea Ferroglia, Ben D. Pecjak, Adrian Signer, Li Lin Yang

Publications and Research

We consider soft gluon emission corrections to the production of a top-antitop pair in association with a Higgs boson at hadron colliders. In particular, we present a softgluon resummation formula for this production process and gather all elements needed to evaluate it at next-to-next-to-leading logarithmic order. We employ these results to obtain approximate next-to-next-to-leading order (NNLO) formulas, and implement them in a bespoke parton-level Monte Carlo program which can be used to calculate the total cross section along with arbitrary differential distributions. We use this tool to study the phenomenological impact of the approximate NNLO corrections, finding that they increase …

Soft Robotic Grippers For Biological Sampling On Deep Reefs, Kevin C. Galloway, Kaitlyn P. Becker, Brennan Phillips, Jordan Kirby, Stephen Licht, Dan Tchernov, Robert J. Wood, David F. Gruber

Publications and Research

This article presents the development of an underwater gripper that utilizes soft robotics technology to delicately manipulate and sample fragile species on the deep reef. Existing solutions for deep sea robotic manipulation have historically been driven by the oil industry, resulting in destructive interactions with undersea life. Soft material robotics relies on compliant materials that are inherently impedance matched to natural environments and to soft or fragile organisms. We demonstrate design principles for soft robot end effectors, bench-top characterization of their grasping performance, and conclude by describing in situ testing at mesophotic depths. The result is the first use of …

Sefo: A Package For Generating Probabilistic Forecasts From Nmme Predictive Ensembles, Nir Krakauer

Publications and Research

Long-range weather forecasts based on output from ensembles of computer simulations are attracting increasing interest. A variety of methods have been proposed to convert the ensemble outputs to calibrated probabilistic forecasts. The package presented here (SeFo, for Seasonal Forecasting) implements a number of methods for producing forecasts of monthly surface air temperature anomalies up to 9 months in advance using output from the North American Multi-Model Ensemble (NMME). The package contains modules for downloading and reading past observations and ensemble output; producing forecast probability distributions; and verifying and calibrating a user-determined subset of methods using arbitrary past periods. By changing …

Controlled Microfluidics To Examine Growth-Factor Induced Migration Of Neural Progenitors In The Drosophila Visual System, Cade Beck, Tanya Singh, Angela Farooqi, Tadmiri Venkatesh, Maribel Vazquez

Publications and Research

BACKGROUND:

The developing visual system in Drosophila melanogaster provides an excellent model with which to examine the effects of changing microenvironments on neural cell migration via microfluidics, because the combined experimental system enables direct genetic manipulation, in vivo observation, and in vitro imaging of cells, post-embryo. Exogenous signaling from ligands such as fibroblast growth factor (FGF) is well-known to control glia differentiation, cell migration, and axonal wrapping central to vision.

NEW METHOD:

The current study employs a microfluidic device to examine how controlled concentration gradient fields of FGF are able to regulate the migration of vision-critical glia cells with and …

Stable Topological Insulators Achieved Using High Energy Electron Beams, Lukas Zhao, Marcin Konczykowski, Haiming Deng, Inna Korzhovska, Milan Begliarbekov, Zhiyi Chen, Evangelos Papalazarou, Marino Marsi, Luca Perfetti, Andrzej Hruban, Agnieszka Wolos, Lia Krusin-Elbaum

Publications and Research

Topological insulators are potentially transformative quantum solids with metallic surface states which have Dirac band structure and are immune to disorder. Ubiquitous charged bulk defects, however, pull the Fermi energy into the bulk bands, denying access to surface charge transport. Here we demonstrate that irradiation with swift (B2.5MeV energy) electron beams allows to compensate these defects, bring the Fermi level back into the bulk gap and reach the charge neutrality point (CNP). Controlling the beam fluence, we tune bulk conductivity from p- (hole-like) to n-type (electron-like), crossing the Dirac point and back, while preserving the Dirac energy dispersion. The CNP …

Performance Modeling Of Cmos Inverters Using Support Vector Machines (Svm) And Adaptive Sampling, Ashwin Satyanarayana

Publications and Research

Integrated circuit designs are verified through the use of circuit simulators before being reproduced in real silicon. In order for any circuit simulation tool to accurately predict the performance of a CMOS design, it should generate models to predict the transistor’s electrical characteristics. The circuit simulation tools have access to massive amounts of data that are not only dynamic but generated at high speed in real time, hence making fast simulation a bottleneck in integrated circuit design. Using all the available data is prohibitive due to memory and time constraints. Accurate and fast sampling has been shown to enhance processing …

Experimental Demonstration Of Topological Effects In Bianisotropic Metamaterials, Alexey P. Slobozhanyuk, Alexander B. Khanikaev, Dmitry S. Filonov, Daria A. Smirnova, Andrey E. Miroshnichenko, Yuri S. Kivshar

Publications and Research

Existence of robust edge states at interfaces of topologically dissimilar systems is one of the most fascinating manifestations of a novel nontrivial state of matter, a topological insulator. Such nontrivial states were originally predicted and discovered in condensed matter physics, but they find their counterparts in other fields of physics, including the physics of classical waves and electromagnetism. Here, we present the first experimental realization of a topological insulator for electromagnetic waves based on engineered bianisotropic metamaterials. By employing the near-field scanning technique, we demonstrate experimentally the topologically robust propagation of electromagnetic waves around sharp corners without backscattering effects.

Predicted Molecular Signaling Guiding Photoreceptor Cell Migration Following Transplantation Into Damaged Retina, Uchenna John Unachukwu, Alice Warren, Ze Li, Shawn Mishra, Jing Zhou, Moira Sauane, Hyungsik Lim, Maribel Vazquez, Stephen Redenti

Publications and Research

To replace photoreceptors lost to disease or trauma and restore vision, laboratories around the world are investigating photoreceptor replacement strategies using subretinal transplantation of photoreceptor precursor cells (PPCs) and retinal progenitor cells (RPCs). Significant obstacles to advancement of photoreceptor cell-replacement include low migration rates of transplanted cells into host retina and an absence of data describing chemotactic signaling guiding migration of transplanted cells in the damaged retinal microenvironment. To elucidate chemotactic signaling guiding transplanted cell migration, bioinformatics modeling of PPC transplantation into light-damaged retina was performed. The bioinformatics modeling analyzed whole-genome expression data and matched PPC chemotactic cell-surface receptors to …

Sulfur-Mediated Photochemical Energy Harvesting In Nanoporous Carbons, Alicia Gomis-Berenguer, Mykola Seredych, Jesus Iniesta, Joao C. Lima, Teresa J. Bandosz, Conchi O. Ania

Publications and Research

This work provides new insights in the field of applied photochemistry based on semiconductor-free nanoporous carbons and its application to sunlight energy harvesting. Using carbon materials of increasing average pore size, chemical functionalization to introduce a variety of O- and S-containing functional groups and monochromatic light, we have shown the dependence of the photochemical conversion of phenol in the confinement of the carbons nanopore space with the wavelength of the irradiation source, the dimensions of the pore voids and their surface chemistry. The photochemical conversion of phenol inside the carbons pore space was found to be very sensitive to the …

Age And Employee Green Behaviors: A Meta-Analysis, Brenton M. Wiernik, Stephan Dilchert, Deniz S. Ones

Publications and Research

Recent economic and societal developments have led to an increasing emphasis on organizational environmental performance. At the same time, demographic trends are resulting in increasingly aging labor forces in many industrialized nations. Commonly held stereotypes suggest that older workers are less likely to be environmentally responsible than younger workers. To evaluate the degree to which such age differences are present, we meta-analyzed 132 independent correlations and 336 d-values based on 4676 professional workers from 22 samples in 11 countries. Contrary to popular stereotypes, age showed small positive relationships with pro-environmental behaviors, suggesting that older adults engaged in these workplace …

Testing Create At Community Colleges: An Examination Of Faculty Perspectives And Diverse Student Gains, Kristy L. Kenyon, Morgan E. Onorato, Alan J. Gottesman, Jamila Hoque, Sally G. Hoskins

Publications and Research

CREATE (Consider, Read, Elucidate the hypotheses, Analyze and interpret the data, and Think of the next Experiment) is an innovative pedagogy for teaching science through the intensive analysis of scientific literature. Initiated at the City College of New York, a minority-serving institution, and regionally expanded in the New York/New Jersey/Pennsylvania area, this methodology has had multiple positive impacts on faculty and students in science, technology, engineering, and mathematics courses. To determine whether the CREATE strategy is effective at the community college (2-yr) level, we prepared 2-yr faculty to use CREATE methodologies and investigated CREATE implementation at community colleges in seven …

Improving Landslide Hazard And Risk Mapping In Guatemala Using Terrain Aspect, Yuri Gorohkovich, Elia Axinia Machado, Luis Ivan Giron Melgar, Mahta Ghahremani

Publications and Research

Guatemala is in the path of numerous atmospheric hazards that trigger landslides by saturating mountain slopes with water reducing their safety factor. Available local studies of landslide characterization in Guatemala have indicated the importance of slope in hazard and risk mapping, but, for the most part, ignored another topographic index: aspect. However, many regional studies analyzing the effect of hurricanes on terrain show that Caribbean and Central American locations experience higher impact from hurricanes and storms on eastern, southeastern, southern and southwestern slopes. Since hazard and risk mapping focuses on infrastructure and settlements located on slopes with various orientations, this …

Towards Improving Interface Modularity In Legacy Java Software Through Automated Refactoring, Raffi T. Khatchadourian, Olivia Moore, Hidehiko Masuhara

Publications and Research

The skeletal implementation pattern is a software design pattern consisting of defining an abstract class that provides a partial interface implementation. However, since Java allows only single class inheritance, if implementers decide to extend a skeletal implementation, they will not be allowed to extend any other class. Also, discovering the skeletal implementation may require a global analysis. Java 8 enhanced interfaces alleviate these problems by allowing interfaces to contain (default) method implementations, which implementers inherit. Java classes are then free to extend a different class, and a separate abstract class is no longer needed; developers considering implementing an interface need …

Towards Improving Interface Modularity In Legacy Java Software Through Automated Refactoring, Raffi Khatchadourian, Olivia Moore, Hidehiko Masuhara

Publications and Research

The skeletal implementation pattern is a software design pattern that defines an abstract class that provides a partial interface implementation. However, since Java allows only single class inheritance, if implementers decide to extend a skeletal implementation, they will not be allowed to extend any other class. Also, discovering the skeletal implementation may require a global analysis. Java 8 enhanced interfaces alleviate these problems by enabling interfaces to contain (default) method implementations, which implementers inherit. Java classes are then free to extend a different class, and a separate abstract class is no longer needed; developers considering implementing an interface need only …

Classification Accuracy Of Mixed Format Tests: A Bi-Factor Item Response Theory Approach, Wei Wang, Fritz Drasgow, Liwen Liu

Publications and Research

Mixed format tests (e.g., a test consisting of multiple-choice [MC] items and constructed response [CR] items) have become increasingly popular. However, the latent structure of item pools consisting of the two formats is still equivocal. Moreover, the implications of this latent structure are unclear: For example, do constructed response items tap reasoning skills that cannot be assessed with multiple choice items? This study explored the dimensionality of mixed format tests by applying bi-factor models to 10 tests of various subjects from the College Board’s Advanced Placement (AP) Program and compared the accuracy of scores based on the bi-factor analysis with …

How Much Should You Pay For A Financial Derivative?, Boyan Kostadinov

Publications and Research

We explain some key mathematical ideas behind the no-arbitrage pricing of financial derivatives by replication, starting from a simple coin toss model and ending with the continuous-time limit of a multi-step coin-toss model using a geometric random walk model. In the limit, we obtain the classical Black-Scholes-Merton formula for pricing European call and put options.

750 Gev Diphotons From Closed String States, Luis Anchordoqui, Ignatios Antoniadis, Haim Goldberg, Xing Huang, Dieter Lüst, Tomasz R. Taylor

Publications and Research

We show that low-mass-scale string compactifications, with a generic D-brane configuration that realizes the standard model by open strings, can explain the relatively broad peak in the diphoton invariant mass spectrum at 750GeV recently reported by the ATLAS and CMS Collaborations. Under reasonable assumptions, we demonstrate that the excess could originate from a closed string (possibly axionic) excitation ϕthat has a coupling with gauge kinetic terms. We estimate the ϕ production rate from photon–photon fusion in elastic pp scattering, using the effective photon and narrow width approximations. For string scales above today’slower limit Ms≈7TeV, we can accommodate the diphoton rate …

Plasmon Excitations Of Multilayer Graphene On A Conducting Substrate, Godfrey Gumbs, Abdrii Iurov, Jhao-Ying Wu, M. F. Lin, Paula Fekete

Publications and Research

We predict the existence of low-frequency nonlocal plasmons at the vacuum-surface interface of a superlattice of N graphene layers interacting with conducting substrate. We derive a dispersion function that incorporates the polarization function of both the graphene monolayers and the semi-infinite electron liquid at whose surface the electrons scatter specularly. We find a surface plasmon-polariton that is not damped by particle-hole excitations or the bulk modes and which separates below the continuum mini-band of bulk plasmon modes. The surface plasmon frequency of the hybrid structure always lies below s = p/ 2, the surface plasmon frequency of the conducting substrate. …

Cogenerative Dialogue: Developing Biology Learning Accommodations For Students With Disabilities, Edward Lehner

Publications and Research

A prominent challenge, at times under-addressed in the science education literature, is considering what types of learning accommodations science teachers should employ for students with disabilities. Outside of science education, researchers have consistently outlined how Universal Design for Learning (UDL) is one efficient means by which to engage students with disabilities in the curriculum. This paper presents the results of a research study in which teachers employed cogenerative dialogue as a learning space where UDL was used to differentiate and individualize instruction in an inclusive biology class. The data originated from a larger, ongoing, longitudinal ethnography of science learning in …

Brane Brick Models, Toric Calabi-Yau 4-Folds And 2d (0,2) Quivers, Sebastian Franco, Sangmin Lee, Rak-Kyeong Seong

Publications and Research

We introduce brane brick models, a novel type of Type IIA brane congurations consisting of D4-branes ending on an NS5-brane. Brane brick models are T-dual to D1-branes over singular toric Calabi-Yau 4-folds. They fully encode the innite class of 2d (generically) N = (0; 2) gauge theories on the worldvolume of the D1-branes and streamline their connection to the probed geometries. For this purpose, we also introduce new combinatorial procedures for deriving the Calabi-Yau associated to a given gauge theory and vice versa.

Design And Analysis Of A Single-Camera Omnistereo Sensor For Quadrotor Micro Aerial Vehicles (Mavs), Carlos Jaramillo, Roberto G. Valenti, Ling Guo, Jizhong Xiao

Publications and Research

We describe the design and 3D sensing performance of an omnidirectional stereo (omnistereo) vision system applied to Micro Aerial Vehicles (MAVs). The proposed omnistereo sensor employs a monocular camera that is co-axially aligned with a pair of hyperboloidal mirrors (a vertically-folded catadioptric configuration). We show that this arrangement provides a compact solution for omnidirectional 3D perception while mounted on top of propeller-based MAVs (not capable of large payloads). The theoretical single viewpoint (SVP) constraint helps us derive analytical solutions for the sensor’s projective geometry and generate SVP-compliant panoramic images to compute 3D information from stereo correspondences (in a truly synchronous …

A Novel Compressed Sensing Method For Magnetic Resonance Imaging: Exponential Wavelet Iterative Shrinkage-Thresholding Algorithm With Random Shift, Yudong Zhang, Jiquan Yang, Jianfei Yang, Aijun Liu, Ping Sun

Publications and Research

Aim. It can help improve the hospital throughput to accelerate magnetic resonance imaging (MRI) scanning. Patients will benefit from less waiting time. Task. In the last decade, various rapid MRI techniques on the basis of compressed sensing (CS) were proposed. However, both computation time and reconstruction quality of traditional CS-MRI did not meet the requirement of clinical use.

Method. In this study, a novel method was proposed with the name of exponential wavelet iterative shrinkagethresholding algorithm with random shift (abbreviated as EWISTARS). It is composed of three successful components: (i) exponential wavelet transform, (ii) iterative shrinkage-thresholding algorithm, and (iii) randomshift. …

How To Measure Metallicity From Five-Band Photometry With Supervised Machine Learning Algorithms, Viviana Acquaviva

Publications and Research

We demonstrate that it is possible to measure metallicity from the SDSS five-band photometry to better than 0.1 dex using supervised machine learning algorithms. Using spectroscopic estimates of metallicity as ground truth, we build, optimize and train several estimators to predict metallicity. We use the observed photometry, as well as derived quantities such as stellar mass and photometric redshift, as features, and we build two sample data sets at median redshifts of 0.103 and 0.218 and median r-band magnitude of 17.5 and 18.3, respectively. We find that ensemble methods, such as random forests of trees and extremely randomized trees and …

Supplemental Instruction For Developmental Mathematics: Two-Year Summary, Olen Dias, Alice W. Cunningham, Loreto Porte

Publications and Research

Supplemental instruction—using trained peer tutors to conduct additional class sessions in a group-work format—has been in use for over forty years. However, its success in developmental mathematics has been inconclusive. In the two years since institution of the strategy for developmental mathematics students at Hostos Community College, overall results (n = 5403 students) show significantly improved course pass rates to at least a 99% confidence level. Although no significant course retention differences have yet appeared, academic success itself promotes future retention. The program has proved beneficial for the College’s developmental mathematics students and is being expanded. Future research including …

A Preliminary Assessment Of Gpm-Based Multi-Satellite Precipitation Estimates Over A Monsoon Dominated Region, Satya Prakash, Ashis K. Mitra, Amir Aghakouchak, Zhong Liu, Hamidreza Norouzi, D. S. Pai

Publications and Research

Following the launch of the Global Precipitation Measurement (GPM) Core Observatory, two advanced high resolution multi-satellite precipitation products namely, Integrated Multi-satellitE Retrievals for GPM (IMERG) and Global Satellite Mapping of Precipitation (GSMaP) version 6 are released. A critical evaluation of these newly released precipitation data sets is very important for both the end users and data developers. This study provides a comprehensive assessment of IMERG research product and GSMaP estimates over India at a daily scale for the southwest monsoon season (June to September 2014). The GPM-based precipitation products are inter-compared with widely used TRMM Multi-satellite Precipitation Analysis (TMPA), and …

Improved Viirs And Modis Sst Imagery, Irina Gladkova, Alexander Ignatov, Fazlul Shahriar, Yury Kihai, Don Hillger, Boris Petrenko

Publications and Research

Moderate Resolution Imaging Spectroradiometers (MODIS) and Visible Infrared Imaging Radiometer Suite (VIIRS) radiometers, flown onboard Terra/Aqua and Suomi National Polar-orbiting Partnership (S-NPP)/Joint Polar Satellite System (JPSS) satellites, are capable of providing superior sea surface temperature (SST) imagery. However, the swath data of these multi-detector sensors are subject to several artifacts including bow-tie distortions and striping, and require special pre-processing steps. VIIRS additionally does two irreversible data reduction steps onboard: pixel aggregation (to reduce resolution changes across the swath) and pixel deletion, which complicate both bow-tie correction and destriping. While destriping was addressed elsewhere, this paper describes an algorithm, adopted in …

Impact Of Particle Shape On Electron Transport And Lifetime In Zinc Oxide Nanorod-Based Dye-Sensitized Solar Cells, Roger Chang, Kemakorn Ithisuphalap, Ilona Kretzschmar

Publications and Research

Owing to its high electron mobility, zinc oxide represents a promising alternative to titanium dioxide as the working electrode material in dye-sensitized solar cells (DSCs). When zinc oxide is grown into 1-D nanowire arrays and incorporated into the working electrode of DSCs, enhanced electron dynamics and even a decoupling of electron transport (τd) and electron lifetime (τn) have been observed. In this work, DSCs with working electrodes composed of solution-grown, unarrayed ZnO nanorods are investigated. In order to determine whether such devices give rise to similar decoupling, intensity modulated photocurrent and photovoltage spectroscopies are used to measure τd and τn, …

The Problematic Pleasures Of Productivity And Efficiency In Goa And Navegador, Nancy M. Foasberg

Publications and Research

Eurogames are a specific subset of modern board games known for mathematical beauty, low conflict and light themes. However, despite their apparent nonviolence, they often use colonial themes. This article argues that the uncritical embrace of these themes and "abstracting away" of troubling historical content results in a narrative that supports colonialism. Two examples of the genre, Goa and Navegador are analyzed in detail.

Pore Structure And Synergy In Antimicrobial Peptides Of The Magainin Family, Almudena Pino-Angeles, John M. Leveritt Iii, Themis Lazaridis

Publications and Research

Magainin 2 and PGLa are among the best-studied cationic antimicrobial peptides. They bind preferentially to negatively charged membranes and apparently cause their disruption by the formation of transmembrane pores, whose detailed structure is still unclear. Here we report the results of 5–9 μs all-atom molecular dynamics simulations starting from tetrameric transmembrane helical bundles of these two peptides, as well as their stoichiometric mixture, and the analog MG-H2 in DMPC or 3:1 DMPC/DMPG membranes. The simulations produce pore structures that appear converged, although some effect of the starting peptide arrangement (parallel vs. antiparallel) is still observed on this timescale. The peptides …