Digital Commons Network^™

Rezina Shams – The First Known Woman Geologist From Dhaka University (Bangladesh) To Obtain A Phd, Nazrul I. Khandaker

Publications and Research

Rezina Shams (Dhaka University geology graduate 1985; née Rezina Bashar) is the first known female geologist from Bangladesh to obtain a PhD in 1991 (University of Birmingham, UK). Rezina’s undergraduate and graduate education in geology at Dhaka University (DU) was at a time when only a handful of female students attended the program. Rezina’s debut into her geology career began with the Master Plan Organisation (MPO) and then the Bangladesh Atomic Energy Commission (1986). Rezina kept her aspirations alive, and eventually furthered her geoscience education to a PhD. Upon receiving a PhD in 1991 from the University of Birmingham under …

Experimental Observation Of Topological Z2 Excitonpolaritons In Transition Metal Dichalcogenide Monolayers, Mengyao Li, Ivan Sinev, Fedor Benimetskiy, Tatyana Ivanova, Ekaterina Khestanova, Svetlana Kiriushechkina, Anton Vakulenko, Sriram Guddala, Maurice Skolnick, Vinod M. Menon, Dmitry Krizhanovskii, Andrea Alù, Anton Samusev, Alexander B. Khanikaev

Publications and Research

The rise of quantum science and technologies motivates photonics research to seek new platforms with strong light-matter interactions to facilitate quantum behaviors at moderate light intensities. Topological polaritons (TPs) offer an ideal platform in this context, with unique properties stemming from resilient topological states of light strongly coupled with matter. Here we explore polaritonic metasurfaces based on 2D transition metal dichalcogenides (TMDs) as a promising platform for topological polaritonics. We show that the strong coupling between topological photonic modes of the metasurface and excitons in TMDs yields a topological polaritonic Z₂ phase. We experimentally confirm the emergence of one-way …

A Vision For Science Gateways: Bridging The Gap And Broadening The Outreach, Sandra Gesing, Steven R. Brandt, Shannon Bradley, Mark Potkewitz, Kirk F. Kee, Noreen Y. Whysel, Mark J. Perri, Sean B. Cleveland, Annalie Rugg, Jack A. Smith

Publications and Research

The future for science gateways warrants exploration as we consider the possibilities that extend well beyond science and high performance computing into new interfaces, applications and user communities. In this paper, we look retrospectively at the successes of representative gateways thus far. This serves to highlight existing gaps gateways need to overcome in areas such as accessibility, usability and interoperability, and in the need for broader outreach by drawing insights from technology adoption research. We explore two particularly promising opportunities for gateways - computational social sciences and virtual reality – and make the case for the gateway community to be …

Quo Vadis Lakes Azuei And Enriquillo: A Future Outlook For Two Of The Caribbean Basin's Largest Lakes, Mahrokh Moknatian, Michael Piasecki

Publications and Research

Lakes Azuei (LA) and Enriquillo (LE) on Hispaniola Island started expanding in 2005 and continued to do so until 2016. After inundating large swaths of arable land, submerging a small community, and threatening to swallow a significant trade route between the Dominican Republic and Haiti; worries persisted at how far this seemingly unstoppable expansion would go. The paper outlines the approach to a look forward to answer this question vis-à-vis climate change scenarios developed by the Intergovernmental Panel on Climate Change (IPCC). It uses numerical representations of the two lakes, and it examines how the lakes might evolve, deploying three …

Tailoring Exceptional Points In A Hybrid Pt-Symmetric And Anti-Pt-Symmetric Scattering System, Zhicheng Xiao, Andrea Alù

Advanced Science Research Center

Fano resonances feature an asymmetric lineshape with controllable linewidth, stemming from the interplay between bright and dark resonances. They provide efficient opportunities to shape the scattering lineshape, but they usually lack flexibility and tunability and are hindered by loss in passive systems. Here, we explore a hybrid parity-time (PT) and anti-parity-time (APT) symmetric system supporting unitary scattering features with highly tunable Fano resonances. The PT-APT-symmetric system can be envisioned in nanophotonic and microwave circuit implementations, allowing for real-time control of the scattering lineshape and its underlying singularities. Our study shows the opportunities enabled by non-Hermitian platforms to control scattering lineshapes …

On Communication For Distributed Babai Point Computation, Maiara F. Bollauf, Vinay A. Vaishampayan, Sueli I.R. Costa

Publications and Research

We present a communication-efficient distributed protocol for computing the Babai point, an approximate nearest point for a random vector X∈Rn in a given lattice. We show that the protocol is optimal in the sense that it minimizes the sum rate when the components of X are mutually independent. We then investigate the error probability, i.e. the probability that the Babai point does not coincide with the nearest lattice point, motivated by the fact that for some cases, a distributed algorithm for finding the Babai point is sufficient for finding the nearest lattice point itself. Two different probability models for X …

Graph-Theoretic Partitioning Of Rnas And Classification Of Pseudoknots-Ii, Louis Petingi

Publications and Research

Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called blocks and determine whether each block contains a pseudoknot or not. As pseudoknots can not be contained into two different blocks, this characterization allow us to efficiently isolate smaller RNA fragments and classify them as pseudoknotted or pseudoknot-free regions, while keeping these sub-structures intact. Moreover we have extended the partitioning algorithm by classifying a pseudoknot as either recursive or non-recursive in order to continue with our research …

Decoding Clinical Biomarker Space Of Covid-19: Exploring Matrix Factorization-Based Feature Selection Methods, Farshad Saberi-Movahed, Mahyar Mohammadifard, Adel Mehrpooya, Mohammad Rezaei-Ravari, Kamal Berahmand, Mehrdad Rostami, Saeed Karami, Mohammad Najafzadeh, Davood Hajinezhad, Mina Jamshidi, Farshid Abedi, Mahtab Mohammadifard, Elnaz Farbod, Farinaz Safavi, Mohammadreza Dorvash, Shahrzad Vahedi, Mahdi Eftekhari, Farid Saberi-Movahed, Iman Tavassoly

Publications and Research

One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients’ characteristics are usually utilized to identify those patients who need more critical care. However, the clinical evidence shows an unmet need to determine more accurate and optimal clinical biomarkers to triage patients under a condition like the COVID-19 crisis. Here we have presented a machine learning approach to find a group of clinical indicators from the blood tests of a set of COVID-19 …

Predicting Synchronized Gene Coexpression Patterns From Fibration Symmetries In Gene Regulatory Networks In Bacteria, Ian Leifer, Mishael Sánchez‑Pérez, Cecilia Ishida, Hernán A. Makse

Publications and Research

Background: Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Here we address the question whether it is possible to predict gene synchronization from network structure alone. We have recently shown that synchronized gene expression can be predicted from symmetries in the gene regulatory networks described by the concept of symmetry fibrations. We showed that symmetry fibrations partition the genes into groups called fibers based on the symmetries of their ’input trees’, the set of paths in the network through which …

Geologist Syed Humayun Akhter Is Leading The Bangladesh Open University, Nazrul I. Khandaker

Publications and Research

No abstract provided.

Pattern Of Use Of Electronic Health Record (Ehr) Among The Chronically Ill: A Health Information National Trend Survey (Hints) Analysis, Rose Calixte, Sumaiya Islam, Zainab Toteh Osakwe, Argelis Rivera, Marlene Camacho-Rivera

Publications and Research

Effective patient–provider communication is a cornerstone of patient-centered care. Patient portals provide an effective method for secure communication between patients or their proxies and their health care providers. With greater acceptability of patient portals in private practices, patients have a unique opportunity to manage their health care needs. However, studies have shown that less than 50% of patients reported accessing the electronic health record (EHR) in a 12-month period. We used HINTS 5 cycle 1 and cycle 2 to assess disparities among US residents 18 and older with any chronic condition regarding the use of EHR for secure direct messaging …

Acute Effect Of High‑Definition And Conventional Tdcs On Exercise Performance And Psychophysiological Responses In Endurance Athletes: A Randomized Controlled Trial, Daniel Gomes Da Silva Machado, Marom Bikson, Abhishek Datta, Egas Caparelli‑Dáquer, Gozde Unal, Abrahão F. Baptista, Edilson Serpeloni Cyrino, Li Min Li, Edgard Morya, Alexandre Moreira, Alexandre Hideki Okano

Publications and Research

Transcranial direct current stimulation (tDCS) has been used aiming to boost exercise performance and inconsistent findings have been reported. One possible explanation is related to the limitations of the so-called “conventional” tDCS, which uses large rectangular electrodes, resulting in a diffuse electric field. A new tDCS technique called high-definition tDCS (HD-tDCS) has been recently developed. HD-tDCS uses small ring electrodes and produces improved focality and greater magnitude of its aftereffects. This study tested whether HD-tDCS would improve exercise performance to a greater extent than conventional tDCS. Twelve endurance athletes (29.4 ± 7.3 years; 60.15 ± 5.09 ml kg− 1 min− …

Fingerprinting The Cretaceous-Paleogene Boundary Impact With Zn Isotopes, Ryan Mathur, Brandon Mahan, Marissa Spencer, Linda Godfrey, Neil Landman, Matthew Garb, D. Graham Pearson, Sheng-Ao Liu, Francisca E. Oboh-Ikuenobe

Publications and Research

Numerous geochemical anomalies exist at the K-Pg boundary that indicate the addition of extraterrestrial materials; however, none fingerprint volatilization, a key process that occurs during large bolide impacts. Stable Zn isotopes are an exceptional indicator of volatilityrelated processes, where partial vaporization of Zn leaves the residuum enriched in its heavy isotopes. Here, we present Zn isotope data for sedimentary rock layers of the K-Pg boundary, which display heavier Zn isotope compositions and lower Zn concentrations relative to surrounding sedimentary rocks, the carbonate platform at the impact site, and most carbonaceous chondrites. Neither volcanic events nor secondary alteration during weathering and …

7 Strategies To Make Professional Development Successful, Marla A. Sole

Publications and Research

Highly effective teachers continually innovate and refine their pedagogical practices through professional development. Committed teachers are interested in professional development that demonstrates best practices aligned with the content they are teaching and clearly communicates the steps, benefits, and challenges of implementing new lessons and innovative practices. Those running workshops can gain valuable insight into teachers’ classroom practices, the curriculum, and potential modifications that could better help students reach their full potential.

21st Century Ecopoetics And Ecotheory, Robert Balun

Open Educational Resources

Ecopoetics is the study of literature that is concerned with ecology and nature. However, beyond just literature about nature, this course will examine how ecology and nature have become complicated in the 21st century, the age of the Anthropocene, the age of the climate crisis and the 6th mass extinction (don’t worry, we will define these and other key terms).

In the 21st century, humans are now confronted with a growing awareness of their destructive impact on the earth, its environments, and its human and non-human inhabitants. In this class we will examine how ecology and nature have become complicated …

Covid-19 Impact On Radiology Students’ Distance Learning (Summer 2021), Mary Lee, Jason Chan, Cheryann Jackson-Holmes, Renzo Marmolejo, Zoya Vinokur

Publications and Research

The Radiological Technology students have adjusted from the urgent distance learning that was enacted in the Spring of 2020, to the hybrid distance learning that is currently in place. This hybrid distance learning is the same way the incoming class of radiological technology students were taught. Both cohorts of students were tracked over the year by online anonymous surveys. We wanted to know how students were adapting to distance learning, if their focus and motivation varied over the course of the year due to changing pandemic conditions. For the students that were working, what impact did it have on their …

Dynamic Parameter Estimation From Partial Observations Of The Lorenz System, Eunice Ng

Theses and Dissertations

Recent numerical work of Carlson-Hudson-Larios leverages a nudging-based algorithm for data assimilation to asymptotically recover viscosity in the 2D Navier-Stokes equations as partial observations on the velocity are received continuously-in-time. This "on-the-fly" algorithm is studied both analytically and numerically for the Lorenz equations in this thesis.

Smooth Global Approximation For Continuous Data Assimilation, Kenneth R. Brown

Theses and Dissertations

This thesis develops the finite element method, constructs local approximation operators, and bounds their error. Global approximation operators are then constructed with a partition of unity. Finally, an application of these operators to data assimilation of the two-dimensional Navier-Stokes equations is presented, showing convergence of an algorithm in all Sobolev topologies.

The Exact Factorization Equations For One- And Two-Level Systems, Bart Rosenzweig

Theses and Dissertations

Exact Factorization is a framework for studying quantum many-body problems. This decomposes the wavefunctions of such systems into conditional and marginal components. We derive corresponding evolution equations for molecular systems whose conditional electronic subsystems are described by one or two Born-Oppenheimer levels and develop a program for their mathematical study.

Lab Exercises For Statistics Using Excel, Julia Nebia, Steven Cosares, Milena Cuellar

Open Educational Resources

This document contains the text associated with a series of computer-based lab exercises to help students apply the concepts usually included in a first course in Statistics. A compressed file has been included that contains a separate folder for each lab. In each folder is an excel spreadsheet file and an editable word document providing the instructions for students to complete the exercise. The exercises are not numbered in the folders, so you can select any subset of these exercises to assign to your students. You are free to modify the instructions in any way you see fit, e.g., to …

Precoder Design For Communication-Efficient Distributed Mimo Receivers With Controlled Peak-Average Power Ratio, Vinay A. Vaishampayan

Publications and Research

We consider the problem of communicating over a relay-assisted multiple-input multiple-output (MIMO) channel with additive noise, in which physically separated relays forward quantized information to a central decoder where the transmitted message is to be decoded. We assume that channel state information is available in the transmitter and show that the design of a rational-forcing precoder - a precoder which is matched to the quantizers used in the relays - is beneficial for reducing the symbol error probability. It turns out that for such rational-forcing precoder based systems, there is natural tradeoff between the peak to average power ratio in …

Direct Observation Of Chaotic Resonances In Optical Microcavities, Shuai Wang, Shuai Liu, Yilin Liu, Shumin Xiao, Zi Wang, Yubin Fan, Jiecai Han, Li Ge, Qinghai Song

Publications and Research

Optical microcavities play a significant role in the study of classical and quantum chaos. To date, most experimental explorations of their internal wave dynamics have focused on the properties of their inputs and outputs, without directly interrogating the dynamics and the associated mode patterns inside. As a result, this key information is rarely retrieved with certainty, which significantly restricts the verification and understanding of the actual chaotic motion. Here we demonstrate a simple and robust approach to directly and rapidly map the internal mode patterns in chaotic microcavities. By introducing a local index perturbation through a pump laser, we report …

Weather And Crime: New York State, Yuna Kim

Student Theses

The present study assesses the degree to which temperature affects the crime rates in all 62 counties in the State of New York. Five different crimes (i.e., robbery, aggravated assault, burglary; larceny, and motor vehicle theft) for the year 2019 were selected from the Division of Criminal Justice Services of New York to be examined. The current study examined whether the rate of these crimes was associated with the changes in weather, with the assumption that higher weathers would lead to higher property and violent crimes, when controlling for the effect of various control variables. The findings suggest that the …

Evaluation Of Log P, Pka, And Log D Predictions From The Sampl7 Blind Challenge, Teresa Danielle Bergazin, Nicolas Tielker, Yingying Zhang, Junjun Mao, M. R. Gunner, Karol Francisco, Carlo Ballatore, Stefan M. Kast, David L. Mobley

Publications and Research

The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges focuses the computational modeling community on areas in need of improvement for rational drug design. The SAMPL7 physical property challenge dealt with prediction of octanol-water partition coefficients and pK_a for 22 compounds. The dataset was composed of a series of N-acylsulfonamides and related bioisosteres. 17 research groups participated in the log P challenge, submitting 33 blind submissions total. For the pK_a challenge, 7 different groups participated, submitting 9 blind submissions in total. Overall, the accuracy of octanol-water log P predictions in the SAMPL7 challenge was …

Sites Of Circadian Clock Neuron Plasticity Mediate Sensory Integration And Entrainment, Maria P. Fernand, Hannah L. Pettibone, Joseph T. Bogart, Casey J. Roell, Charles E. Davey, Ausra Pranevicius, Khang V. Huynh, Sara M. Lennox, Boyan Kostadinov, Orie T. Shafer

Publications and Research

Networks of circadian timekeeping in the brain display marked daily changes in neuronal morphology. In Drosophila melanogaster, the striking daily structural remodeling of the dorsal medial termini of the small ventral lateral neurons has long been hypothesized to mediate endogenous circadian timekeeping. To test this model, we have specifically abrogated these sites of daily neuronal remodeling through the reprogramming of neural development and assessed the effects on circadian timekeeping and clock outputs. Remarkably, the loss of these sites has no measurable effects on endogenous circadian timekeeping or on any of the major output functions of the small ventral lateral neurons. …

Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner

Publications and Research

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome …

Covid-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning, Yang Liu, You Wu, Xiaoke Shen, Lei Xie

Publications and Research

The life-threatening disease COVID-19 has inspired significant efforts to discover novel therapeutic agents through repurposing of existing drugs. Although multi-targeted (polypharmacological) therapies are recognized as the most efficient approach to system diseases such as COVID-19, computational multi-targeted compound screening has been limited by the scarcity of high-quality experimental data and difficulties in extracting information from molecules. This study introduces MolGNN , a new deep learning model for molecular property prediction. MolGNN applies a graph neural network to computational learning of chemical molecule embedding. Comparing to state-of-the-art approaches heavily relying on labeled experimental data, our method achieves equivalent or superior prediction …

Seysl 701 Foundations Of Literacy, Carol Hacker

Open Educational Resources

Syllabus for secondary education teachers of literacy.

The major area of inquiry is the psychological, sociological, cognitive, and linguistic bases of literacy.

Thermal Metasurfaces: Complete Emission Control By Combining Local And Nonlocal Light-Matter Interactions, Adam C. Overvig, Sander A. Mann, Andrea Alù

Advanced Science Research Center

Metasurfaces have been enabling the miniaturization and integration of complex optical functionalities within an ultrathin platform by engineering the scattering features of localized modes. However, these efforts have mostly been limited to the manipulation of externally produced coherent light, e.g., from a laser. In parallel, the past two decades have seen the development of structured surfaces that emit partially coherent radiation via thermally populated, spatially extended (nonlocal) modes. However, the control over thermally emitted light is severely limited compared to optical metasurfaces, and even basic functionalities such as unidirectional emission to an arbitrary angle and polarization remain elusive. Here, we …

Defining The Basis Of Cyanine Phototruncation Enables A New Approach To Single-Molecule Localization Microscopy, Siddharth S. Matikonda, Dominic A. Helmerich, Mara Meub, Gerti Beliu, Philip Kollmannsberger, Alexander Greer, Markus Sauer, Martin J. Schnermann

Publications and Research

The light-promoted conversion of extensively used cyanine dyes to blue-shifted emissive products has been observed in various contexts. However, both the underlying mechanism and the species involved in this photoconversion reaction have remained elusive. Here we report that irradiation of heptamethine cyanines provides pentamethine cyanines, which, in turn, are photoconverted to trimethine cyanines. We detail an examination of the mechanism and substrate scope of this remarkable twocarbon phototruncation reaction. Supported by computational analysis, we propose that this reaction involves a singlet oxygeninitiated multistep sequence involving a key hydroperoxycyclobutanol intermediate. Building on this mechanistic framework, we identify conditions to improve the …