Digital Commons Network^™

Geospatial Resolution Of Human And Bacterial Diversity With City-Scale Metagenomics, Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, Darryl Reeves, Jorge Gandara, Sagar Chhangawala, Sofia Ahsanuddin, Amber Simmons, Timothy Nessel, Bharathi Sundaresh, Elizabeth Pereira, Ellen Jorgensen, Sergios-Orestis Kolokotronis, Nell Kirchberger, Isaac Garcia, David Gandara, Sean Dhanraj, Tanzina Nawrin, Yogesh Saletore, Noah Alexander, Priyanka Vijay, Elizabeth M. Hénaff, Paul Zumbo, Michael Walsh, Gregory D. O'Mullan, Scott Tighe, Joel T. Dudley, Anya Dunaif, Sean Ennis, Eoghan O'Halloran, Tiago R. Magalhaes, Braden Boone, Angela L. Jones, Theodore R. Muth, Katie Schneider Paolantonio, Elizabeth Alter, Eric E. Schadt, Jeanne Garbarino, Robert J. Prill, Jane M. Carlton, Shawn Levy, Christopher E. Mason

Publications and Research

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial …

Population Genetic Structure Of The Dwarf Seahorse (Hippocampus Zosterae) In Florida, Nathan Fedrizzi, Melanie L. J. Stiassny, J. T. Boehm, Eric R. Dougherty, George Amato, Martin Mendez

Publications and Research

The dwarf seahorse (Hippocampus zosterae) is widely distributed throughout near-shore habitats of the Gulf of Mexico and is of commercial significance in Florida, where it is harvested for the aquarium and curio trades. Despite its regional importance, the genetic structure of dwarf seahorse populations remains largely unknown. As an aid to ongoing conservation efforts, we employed three commonly applied mtDNA markers (ND4, DLoop and CO1) to investigate the genetic structuring of H. zosterae in Florida using samples collected throughout its range in the state. A total of 1450 bp provided sufficient resolution to delineate four populations of dwarf seahorses, as …

Serving The Commuter College Student In Urban Academic Libraries, Mariana Regalado, Maura A. Smale

Publications and Research

Cities often host many colleges and universities; while the commuter student in suburban or rural areas may drive or be driven to school, students at colleges and universities in dense, urban settings rely predominantly on mass transit for their commute to class. The act of commuting to campus has been found by a number of researchers to define and shape the experiences of commuter students in college, though the literature on college students who commute is not extensive. A qualitative study of the academic culture and scholarly habits of undergraduate students at the City University of New York (CUNY) revealed …

The Role Mentorship In Supporting African-American Students’ Entry Into Stem Careers, Charles Edwards, Kaemanje Thomas

Publications and Research

African-American students are under-represented in STEM careers. The National Center for Education Statistics (NCES) reported in 2009 that African-American students received 7% of STEM bachelor’s degrees, 4% of master’s degrees and 2% of Ph.Ds. Mentorship programs are identified as one strategy of improving African-American students’ outcomes in STEM careers. The researchers reviewed articles which examine strategies to improve STEM academic and career success. This review focused on exploring the role of mentorship programs in addressing the underrepresentation of African-American students in STEM careers. Despite references to the role of mentorship, the literature reviewed lacked a structured approach for the design …

Inferring Interaction Type In Gene Regulatory Networks Using Co-Expression Data, Pegah Khosravi, Vahid H. Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaei, Gary D. Bader

Publications and Research

Background

Knowledge of interaction types in biological networks is important for understanding the functional organization of the cell. Currently information-based approaches are widely used for inferring gene regulatory interactions from genomics data, such as gene expression profiles; however, these approaches do not provide evidence about the regulation type (positive or negative sign) of the interaction.

Results

This paper describes a novel algorithm, “Signing of Regulatory Networks” (SIREN), which can infer the regulatory type of interactions in a known gene regulatory network (GRN) given corresponding genome-wide gene expression data. To assess our new approach, we applied it to three different benchmark …

A Re-Interpretation Of The Triangulum-Andromeda Stellar Clouds: A Population Of Halo Stars Kicked Out Of The Galactic Disk, Adrian M. Price-Whelan, Kathryn V. Johnston, Allyson A. Sheffield, Chervin F. P. Laporte, Branimir Sesar

Publications and Research

The Triangulum–Andromeda stellar clouds (TriAnd1 and TriAnd2) are a pair of concentric ring- or shell-like overdensities at large R (≈30 kpc) and Z (≈−10 kpc) in the Galactic halo that are thought to have been formed from the accretion and disruption of a satellite galaxy. This paper critically reexamines this formation scenario by comparing the number ratio of RR Lyrae to M giant stars associated with the TriAnd clouds with other structures in the Galaxy. The current data suggest a stellar population for these overdensities (fRR: MG < 0.38 at 95 per cent confidence) quite unlike any of the known satellites of the Milky Way (fRR: MG ≈ 0.5 for the very largest and f …

Mechanotransduction: Use The Force(S), Ewa K. Paluch, Celeste M. Nelson, Nicolas Biais, Ben Fabry, Jens Moeller, Beth L. Pruitt, Carina Wollnik, Galina Kudryasheva, Florian Rehfeldt, Walter Federle

Publications and Research

Mechanotransduction - how cells sense physical forces and translate them into biochemical and biological responses - is a vibrant and rapidly-progressing field, and is important for a broad range of biological phenomena. This forum explores the role of mechanotransduction in a variety of cellular activities and highlights intriguing questions that deserve further attention.

Stably Stratified Canopy Flow In Complex Terrain, Xiyan Xu, Chuixiang Yi, Eric Kutter

Publications and Research

Stably stratified canopy flow in complex terrain has been considered a difficult condition for measuring net ecosystem–atmosphere exchanges of carbon, water vapor, and energy. A long-standing advection error in eddy-flux measurements is caused by stably stratified canopy flow. Such a condition with strong thermal gradient and less turbulent air is also difficult for modeling. To understand the challenging atmospheric condition for eddy-flux measurements, we use the renormalized group (RNG) k–ε turbulence model to investigate the main characteristics of stably stratified canopy flows in complex terrain. In this two-dimensional simulation, we imposed persistent constant heat flux at ground surface and linearly …

Monitoring The Progression Of Spontaneous Articular Cartilage Healing With Infrared Spectroscopy, Megan P. O'Brien, Madhuri Penmatsa, Uday Palukuru, Paul West, Xu Yang, Mathias P. G. Bostrom, Theresa Freeman, Nancy Pleshko

Publications and Research

Objective. Evaluation of early compositional changes in healing articular cartilage is critical for understanding tissue repair and for therapeutic decision-making. Fourier transform infrared imaging spectroscopy (FT-IRIS) can be used to assess the molecular composition of harvested repair tissue. Furthermore, use of an infrared fiber-optic probe (IFOP) has the potential for translation to a clinical setting to provide molecular information in situ. In the current study, we determined the feasibility of IFOP assessment of cartilage repair tissue in a rabbit model, and assessed correlations with gold-standard histology.

Design. Bilateral osteochondral defects were generated in mature white New Zealand rabbits, and …

Focus On Extreme Events And The Carbon Cycle, Chuixiang Yi, Elise Pendall, Philippe Ciais

Publications and Research

Climate physics indicates that warming climate is a likely cause of extreme weather and more frequent and intense climate events. These extreme events can disrupt terrestrial carbon dynamics dramatically by triggering ecological disturbances and potentially forcing climate–carbon feedbacks. In this paper we synthesize the findings of 26 papers that focus on collecting evidence and developing knowledge of how extreme events disturb terrestrial carbon dynamics

Familiarity With And Preferences For Oral And Long-Acting Injectable Hiv Pre-Exposure Prophylaxis (Prep) In A National Sample Of Gay And Bisexual Men In The U.S., Jeffrey T. Parsons, H. Jonathan Rendina, Thomas H.F. Whitfield, Christian Grov

Publications and Research

Objectives: We sought to determine preferences for oral versus long-acting injectable (LAI) PrEP among gay and bisexual men (GBM).

Methods: We surveyed a national U.S. sample of 1,071 GBM about forms of PrEP.

Results: Overall, 46.0% preferred LAI, 14.3% oral, 21.7% whichever was most effective, 10.1% had no preference, and 7.8% would not take PrEP. There were no differences in PrEP preferences by race/ethnicity, income, region of residence, or relationship status. Those unwilling to take PrEP were significantly older than those who preferred LAI PrEP and those who would take either. Those who preferred the most effective …

What You Gotta Know To Play Good In The Iterated Prisoner’S Dilemma, Ethan Akin

Publications and Research

For the iterated Prisoner’s Dilemma there exist good strategies which solve the problem when we restrict attention to the long term average payoff. When used by both players, these assure the cooperative payoff for each of them. Neither player can benefit by moving unilaterally to any other strategy, i.e., these provide Nash equilibria. In addition, if a player uses instead an alternative which decreases the opponent’s payoff below the cooperative level, then his own payoff is decreased as well. Thus, if we limit attention to the long term payoff, these strategies effectively stabilize cooperative behavior. The existence of such strategies …

Search For Patterns By Combining Cosmic-Ray Energy And Arrival Directions At The Pierre Auger Observatory, A. Aab, P. Abreu, M. Aglietta, E. J. Ahn, I. Al Samarai, I. F. M. Albuquerque, I. Allekotte, J. Allen, P. Allison, A. Almela, J. Alvarez Castillo, J. Alvarez-Muñiz, R. Alves Batista, M. Ambrosio, A. Aminaei, L. Anchordoqui, S. Andringa, C. Aramo, V. M. Aranda, F. Arqueros, T. Paul

Publications and Research

Energy-dependent patterns in the arrival directions of cosmic rays are searched for using data of the Pierre Auger Observatory. We investigate local regions around the highest-energy cosmic rays with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$E \ge 6 \times 10^{19}$$\end{document}E≥6×1019 eV by analyzing cosmic rays with energies above \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$E \ge 5 \times 10^{18}$$\end{document}E≥5×1018 eV arriving within an angular separation of approximately 15\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{\circ }$$\end{document}∘. We characterize the energy distributions inside these regions by two independent methods, one searching for angular …

Singly-Spinning Black Rings Ind= 5 U(1)3 Supergravity, H. Lu, C. N. Pope, Justin F. Vázquez-Poritz, Zhibai Zhang

Publications and Research

We construct black ring solutions in five-dimensional U(1)3supergravity which carry three dipole charges, three electric charges and one angular momentum parameter.These solutions are written in a form that is sufficiently compact that their global and thermodynamic properties can be studied explicitly. In particular, we find that the Smarrformula is obeyed regardless of whether or not conical singularities are present, where as the first law of thermodynamics holds only in the absence of conical singularities. We also present black ring solutions with three background magnetic fields.

Maker: Candy Crane Robot, Andy S. Zhang, Angran Xiao, Bijan Bayat Mokhtari

Publications and Research

Candy Crane is a custom-made robot that looks like a traditional tower crane and is used to pick candies by the young users for fun and for learning mechatronics product design. The tower structure is made from either aluminum C-channels or plastics made from 3D printer. Two 12V DC motors and several limit switches are used to control the movement of the crane. A miniature crane to be held by the user is equipped with a linear potentiometer and rotary potentiometer and is used to control the movement of the big tower crane wirelessly through a blue tooth module. An …

Maker: Twisted Sister Rover, Andy S. Zhang, Bryant Vicente, Alexis Daniel Ortiz, Angran Xiao, Anass Baroudi, Albino Marsetti, Rocky Marcus Kowchai

Publications and Research

The Twisted Sister is a four-wheel mobile robot that can twist its front wheels to navigate the rough terrains. Each wheel is driven by a DC motor. The front wheels can be raised by a DC gearmotor which is connected to a worm gear system. The rover chassis is made of sheet metal cut from water jet. An Arduino robot controller is mounted on the Twisted Sister Rover. A remote controller is equipped with two tiny joysticks. One joystick is used to control the movement of the rover and the other joystick to used to either raise or lower the …

Engaging Engineering Experiences For K-5, Melanie L. Villatoro, Servena Narine, Diana Samaroo

Publications and Research

The City University of New York (CUNY) Service Corps mobilizes CUNY students, faculty and staff to work on projects that improve the short and long-term civic, economic and environmental sustainability of New York City and of its residents and communities. Our project was designed to promote A Better Educated City by partnering with Daniel Hale Williams Elementary School; recently designated as a Magnet School for STEM Studies. During the 2014-2015 academic year, two CUNY students worked to develop and implement an Educational Outreach Program which provided children in grades 1-5 with exposure to Science, Technology, Engineering, and Math.

The Energetic Value Of Land-Based Foods In Western Hudson Bayand Their Potential To Alleviate Energy Deficits Of Starving Adult Male Polar Bears, Linda J. Gormezano, Robert F. Rockwell

Publications and Research

Climate change is predicted to expand the ice-free season in western Hudson Bay and when it grows to 180 days, 28–48% of adult male polar bears are projected to starve unless nutritional deficits can be offset by foods consumed on land. We updated a dynamic energy budget model developed by Molnar et al. to allow influx of additional energy from novel terrestrial foods (lesser snow geese, eggs, caribou) that polar bears currently consume as part of a mixed diet while on land. We calculated the units of each prey, alone and in combination, needed to alleviate these lethal energy deficits …

Kinetic Study Of The Oxygen Reduction Reaction On Α-Ni(Oh)2 And Α-Ni(Oh)2 Supported On Graphene Oxide, Elaheh Farjami, L. Jay Deiner

Publications and Research

The kinetics of the oxygen reduction reaction on α-Ni(OH)2 and α-Ni(OH)2 supported on graphene oxide (α-Ni(OH)2/GO) were investigated using rotating disk linear sweep voltammetry in alkaline solutions of varying oxygen and hydroxyl concentrations. Over the full hydroxyl concentration range (0.05 M to 0.5M), α-Ni(OH)2/GO displayed higher activity than unsupported α-Ni(OH)2. The electron transfer numbers were 2.9 ± 0.2 for α-Ni(OH)2, 3.4 ± 0.1 for α-Ni(OH)2/GO at low [OH−], and 3.8–3.9 for α-Ni(OH)2/GO at high [OH−]. Compared to α-Ni(OH)2, α-Ni(OH)2/GO displayed higher chemical reaction rate constants and higher electron transfer rate constants. These differences suggest that the synergy between the α-Ni(OH)2 …

Time Series Analysis For Psychological Research: Examining And Forecasting Change, Andrew T. Jebb, Louis Tay, Wei Wang, Qiming Huang

Publications and Research

Psychological research has increasingly recognized the importance of integrating temporal dynamics into its theories, and innovations in longitudinal designs and analyses have allowed such theories to be formalized and tested. However, psychological researchers may be relatively unequipped to analyze such data, given its many characteristics and the general complexities involved in longitudinal modeling. The current paper introduces time series analysis to psychological research, an analytic domain that has been essential for understanding and predicting the behavior of variables across many diverse fields. First, the characteristics of time series data are discussed. Second, different time series modeling techniques are surveyed that …

Estimates Of Micro-, Nano-, And Picoplankton Contributions To Particle Export In The Northeast Pacific, B. L. Mackinson, S. B. Moran, M. W. Lomas, Gillian M. Stewart, R. P. Kelly

Publications and Research

The contributions of micro-, nano-, and picoplankton to particle export were estimated from measurements of size-fractionated particulate 234Th, organic carbon, and phytoplankton indicator pigments obtained during five cruises between 2010 and 2012 along Line P in the subarctic northeast Pacific Ocean. Sinking fluxes of particulate organic carbon (POC) and indicator pigments were calculated from 234Th;238U disequilibria and, during two cruises, measured by a sediment trap at Ocean Station Papa. POC fluxes at 100m ranged from 0.65 to 7.95 mmolm2 d1, similar in magnitude to previous results at Line P. Microplankton pigments dominate indicator pigment fluxes (averaging 6919% of total pigment …

Mitochondrial Ion Channels In Cancer Transformation, Stephen M. Madamba, Kevin N. Damri, Laurent M. Dejean, Pablo M. Peixoto

Publications and Research

Cancer transformation involves reprograming of mitochondrial function to avert cell death mechanisms, monopolize energy metabolism, accelerate mitotic proliferation, and promote metastasis. Mitochondrial ion channels have emerged as promising therapeutic targets because of their connection to metabolic and apoptotic functions. This mini review discusses how mitochondrial channels may be associated with cancer transformation and expands on the possible involvement of mitochondrial protein import complexes in pathophysiological process.

Evaluation Of Alos Palsar Data For High-Resolution Mapping Of Vegetated Wetlands In Alaska, Daniel Clewley, Jane Whitcomb, Mahta Moghaddam, Kyle Macdonald, Bruce Chapman, Peter Bunting

Publications and Research

As the largest natural source of methane, wetlands play an important role in the carbon cycle. High-resolution maps of wetland type and extent are required to quantify wetland responses to climate change. Mapping northern wetlands is particularly important because of a disproportionate increase in temperatures at higher latitudes. Synthetic aperture radar data from a spaceborne platform can be used to map wetland types and dynamics over large areas. Following from earlier work by Whitcomb et al. (2009) using Japanese Earth Resources Satellite (JERS-1) data, we applied the “random forests” classification algorithm to variables from L-band ALOS PALSAR data for 2007, …

Corrosion Protection Of 304 Stainless Steel With Melting Gels Coatings, Mario Aparicio, Andrei Jitianu, Gabriela Rodriguez, Ahmad Dengah, Kutaiba Marzoki, Jadra Mosa, Lisa C. Klein

Publications and Research

Methyl-substituted melting gels were used to coat AISI 304 stainless steel substrates. Crack-free coatings up to 1 mm in thickness were obtained. SEM micrographs of cross-sections con fi rm good adhesion to the surface. Samples were subjected to structural characterization using FT-IR, and Raman spectroscopy. Mechanical properties were investigated by micro-scratch tests. Electrochemical analyses (anodic polarization and electrochemical impedance spectroscopy) were performed in 3.5% NaCl solutions. Electrochemical tests show excellent performance of the coatings against corrosion with no sign of degradation after several months of immersion.

Using 3d Printed Eggs To Examine The Egg-Rejection Behaviour Of Wild Birds, Branislav Igic, Valerie Nunez, Henning U. Voss, Rebecca Croston, Zachary Aidala, Analía V. López, Aimee Van Tatenhove, Mandë E. Holford, Matthew D. Shawkey, Mark E. Hauber

Publications and Research

The coevolutionary relationships between brood parasites and their hosts are often studied by examining the egg rejection behaviour of host species using artificial eggs. However, the traditional methods for producing artificial eggs out of plasticine, plastic, wood, or plaster-of-Paris are laborious, imprecise, and prone to human error. As an alternative, 3D printing may reduce human error, enable more precise manipulation of egg size and shape, and provide a more accurate and replicable protocol for generating artificial stimuli than traditional methods. However, the usefulness of 3D printing technology for egg rejection research remains to be tested. Here, we applied 3D printing …

Autonomic And Brain Responses Associated With Empathy Deficits In Autism Spectrum Disorder, Xiaosi Gu, Tehila Eilam-Stock, Thomas Zhou, Evdokia Anagnostou, Alexander Kolevzon, Latha Soorya, Patrick R. Hof, Karl J. Friston, Jin Fan

Publications and Research

Accumulating evidence suggests that autonomic signals and their cortical representations are closely linked to emotional processes, and that related abnormalities could lead to social deficits. Although socio-emotional impairments are a defining feature of autism spectrum disorder (ASD), empirical evidence directly supporting the link between autonomic, cortical, and socio-emotional abnormalities in ASD is still lacking. In this study, we examined autonomic arousal indexed by skin conductance responses (SCR), concurrent cortical responses measured by functional magnetic resonance imaging, and effective brain connectivity estimated by dynamic causal modeling in seventeen unmedicated high-functioning adults with ASD and seventeen matched controls while they performed an …

Fully Automated Whole-Head Segmentation With Improved Smoothness And Continuity, With Theory Reviewed, Yu Huang, Lucas C. Parra

Publications and Research

Individualized current-flow models are needed for precise targeting of brain structures using transcranial electrical or magnetic stimulation (TES/TMS). The same is true for current-source reconstruction in electroencephalography and magnetoencephalography (EEG/MEG). The first step in generating such models is to obtain an accurate segmentation of individual head anatomy, including not only brain but also cerebrospinal fluid (CSF), skull and soft tissues, with a field of view (FOV) that covers the whole head. Currently available automated segmentation tools only provide results for brain tissues, have a limited FOV, and do not guarantee continuity and smoothness of tissues, which is crucially important for …

Exploring The Complex Pattern Of Information Spreading In Online Blog Communities, Sen Pei, Lev Muchnik, Shaoting Tang, Zhiming Zheng, Hernán A. Makse

Publications and Research

Information spreading in online social communities has attracted tremendous attention due to its utmost practical values in applications. Despite that several individual-level diffusion data have been investigated, we still lack the detailed understanding of the spreading pattern of information. Here, by comparing information flows and social links in a blog community, we find that the diffusion processes are induced by three different spreading mechanisms: social spreading, self-promotion and broadcast. Although numerous previous studies have employed epidemic spreading models to simulate information diffusion, we observe that such models fail to reproduce the realistic diffusion pattern. In respect to users behaviors, strikingly, …

Using Python To Solve The Navier-Stokes Equations - Applications In The Preconditioned Iterative Methods, Jia Liu, Lina Wu, Xingang Fang

Publications and Research

This article describes a new numerical solver for the Navier-Stokes equations. The proposed solver is written in Python which is a newly developed language. The Python packages are built to solve the Navier-Stokes equations with existing libraries. We have created discretized coefficient matrices from systems of the Navier-Stokes equations by the finite difference method. In addition we focus on the preconditioned Krylov subspace iterative methods in the linearized systems. Numerical results of performances for the Preconditioned iterative methods are demonstrated. The comparison between Python and Matlab is discussed at the end of the paper.

The P -Royden And P -Harmonic Boundaries For Metric Measure Spaces, Marcello Lucia, Michael J. Puls

Publications and Research

Let p be a real number greater than one and let X be a locally compact, noncompact metric measure space that satisfy certain conditions. The p-Royden and p-harmonic boundaries of X are constructed by using the p-Royden algebra of functions on X and a Dirichlet type problem is solved for the p-Royden boundary. We also characterize the metric measure spaces whose p-harmonic boundary is empty.