Digital Commons Network^™

Quertci: A Tool Integrating Github Issue Querying With Comment Classification, Ye Paing, Tatiana Castro Vélez, Raffi Khatchadourian

Publications and Research

Empirical Software Engineering (ESE) researchers study (open-source) project issues and the comments and threads within to discover—among others—challenges developers face when incorporating new technologies, platforms, and programming language constructs. However, such threads accumulate, becoming unwieldy and hindering any insight researchers may gain. While existing approaches alleviate this burden by classifying issue thread comments, there is a gap between searching popular open-source software repositories (e.g., those on GitHub) for issues containing particular keywords and feeding the results into a classification model. This paper demonstrates a research infrastructure tool called QuerTCI that bridges this gap by integrating the GitHub issue comment search …

Recognizing And Disrupting Stigma In Implementation Of Hiv Prevention And Care: A Call To Research And Action, Sarit A. Golub, Rachel A. Fikslin

Publications and Research

Introduction: There is robust evidence that stigma negatively impacts both people living with HIV and those who might benefit from HIV prevention interventions. Within healthcare settings, research on HIV stigma has focused on intra-personal processes (i.e. knowledge or internalization of community-level stigma that might limit clients’ engagement in care) or inter-personal processes (i.e. stigmatized interactions with service providers). Intersectional approaches to stigma call us to examine the ways that intersecting systems of power and oppression produce stigma not only at the individual and interpersonal levels, but also within healthcare service delivery systems. This commentary argues for the importance of analysing …

Oral Anticoagulant Underutilization Among Elderly Patients With Atrial Fibrillation: Insights From The United States Medicare Database, Muhammad Bilal Munir, Patrick Hlavacek, Allison V. Keshishian, Jennifer D. Guo, Rajesh Mallampati, Mauricio Ferri, Cristina Russ, Birol Emir, Matthew Cato, Huseyin Yuce, Jonathan C. Hsu

Publications and Research

Background

Oral anticoagulants (OACs) mitigate stroke risk in patients with atrial fibrillation (AF). The study aim was to analyze prevalence and predictors of OAC underutilization.

Methods

Newly diagnosed AF patients with a CHA2DS2-VASc score ≥ 2 were identified from the US CMS Database (January 1, 2013–December 31, 2017). Patients were stratified based on having an OAC prescription versus not and the OAC prescription group was stratified by direct OAC (DOACs) versus warfarin. Multivariable logistic regression models were used to examine predictors of OAC underutilization.

Results

Among 1,204,507 identified AF patients, 617,611 patients (51.3%) were not prescribed an OAC during follow-up …

Anisotropic Magnetoexcitons In Two-Dimensional Transition Metal Trichalcogenide Semiconductors, Roman Ya. Kezerashvili, Anastasia Spiridonova

Publications and Research

Direct and indirect excitons in Rydberg states in transition metal trichalcogenide (TMTC) monolayers, bilayers, and van der Waals (vdW) heterostructures in an external magnetic field are studied within the framework of the effective mass approximation. Binding energies of magnetoexcitons are calculated using the Rytova-Keldysh potential for direct magnetoexcitons and both the Rytova-Keldysh and Coulomb potentials for indirect magnetoexcitons. We report the magnetic field energy contribution to the binding energies and diamagnetic coefficients for magnetoexcitons that depend strongly on the effective mass anisotropy of electrons and holes. The comparative study of TMTCs and phosphorene is given. In TiS3, TiSe3, and ZrSe3 …

Computer-Aided Response-To-Intervention For Reading Comprehension Based On Recommender System, Ming-Chi Liu, Wei-Yang Lin, Chia-Ling Tsai

Publications and Research

In 2019, New York State Education Department announced 54.6% of all students in grades 3 to 8 not meeting the standard of reading proficiency. Motivated by the need for a more efficient intervention model, we propose a recommender system to leverage the technology in machine learning to recommend suitable reading materials for effective intervention. The recommendation is based on the student's prior reading comprehension assessments and also assessments of other students at the same grade level using collaborative filtering. No other prior academic or demographic information of students is available. Two main challenges are lack of explicit ratings of reading …

Positive Rate-Dependent Action Potential Prolongation By Modulating Potassium Ion Channels, Candido Cabo

Publications and Research

Pharmacological agents that prolong action potential duration (APD) to a larger extent at slow rates than at the fast excitation rates typical of ventricular tachycardia exhibit reverse rate dependence. Reverse rate dependence has been linked to the lack of efficacy of class III agents at preventing arrhythmias because the doses required to have an anti-arrhythmic effect at fast rates may have pro-arrhythmic effects at slow rates due to an excessive APD prolongation. In this report we show that, in computer models of the ventricular action potential, APD prolongation by accelerating phase 2 repolarization (by increasing I_Ks) and decelerating …

Do Book Consumers Discriminate Against Black, Female, Or Young Authors?, Dana B. Weinberg, Adam Kapelner

Publications and Research

The publishing industry shows marked evidence of both gender and racial discrimination. A rational explanation for this difference in treatment of both female and Black authors might relate to the taste-based preferences of book consumers, who might be less willing to pay for books by such authors. We ran a randomized experiment to test for the presence of discriminatory preferences by consumers based on authors’ race, gender and/or age. We collected ratings of 25,201 book surveys across 9,072 subjects on Amazon’s Mechanical Turk, making this study the largest experimental study of the book market to date. Subjects were presented with …

Preconditioned Iteractive Solvers For The 2d Helmholtz Equation Via Radial Basis Functions, Lina Wu

Publications and Research

In this paper, we discuss the solution solver for the linear system of equations arising from the discretized 2D Helmholtz equation using the radial basis functions. The coefficient matrix A that is generated from the discretization is dense and often ill-conditioned. This paper uses preconditioned iterative methods such as the General Minimal Residual method (GMRES) to solve the linear system. Different preconditioners are compared. Numerical experiments are conducted in order to provide a comparison of the convergence rates among various preconditioned linear systems. A further observation is made into the eigenvalue distributions and the choice of the shaping parameters during …

Magnetic-Field-Dependent Stimulated Emission From Nitrogen-Vacancy Centers In Diamond, Felix A. Hahl, Lukas Lindner, Xavier Vidal, Tingpeng Luo, Takeshi Ohshima, Shinobu Onoda, Shuya Ishii, Alexander M. Zaitsev, Marco Capelli, Brant C. Gibson, Andrew D. Greentree, Jan Jeske

Publications and Research

Negatively charged nitrogen-vacancy (NV) centers in diamond are promising magnetic field quantum sensors. Laser threshold magnetometry theory predicts improved NV center ensemble sensitivity via increased signal strength and magnetic field contrast. Here, we experimentally demonstrate laser threshold magnetometry. We use a macroscopic high-finesse laser cavity containing a highly NV-doped and low absorbing diamond gain medium that is pumped at 532 nm and resonantly seeded at 710 nm. This enables a 64% signal power amplification by stimulated emission. We test the magnetic field dependency of the amplification and thus demonstrate magnetic field-dependent stimulated emission from an NV center ensemble. This emission …

Spotlight Report #6: Proffering Machine-Readable Personal Privacy Research Agreements: Pilot Project Findings For Ieee P7012 Wg, Noreen Y. Whysel, Lisa Levasseur

Publications and Research

What if people had the ability to assert their own legally binding permissions for data collection, use, sharing, and retention by the technologies they use? The IEEE P7012 has been working on an interoperability specification for machine-readable personal privacy terms to support this ability since 2018. The premise behind the work of IEEE P7012 is that people need technology that works on their behalf—i.e. software agents that assert the individual’s permissions and preferences in a machine-readable format.

Thanks to a grant from the IEEE Technical Activities Board Committee on Standards (TAB CoS), we were able to explore the attitudes of …

Weakly-Supervised Tumor Purity Prediction From Frozen H&E Stained Slides, Matthew Brendel, Vanesa Getseva, Majd Al Assaad, Michael Sigouros, Alexandros Sigaras, Troy Kane, Pegah Khosravi, Juan Miguel Mosquera, Olivier Elemento, Iman Hajirasouliha

Publications and Research

Background

Estimating tumor purity is especially important in the age of precision medicine. Purity estimates have been shown to be critical for correction of tumor sequencing results, and higher purity samples allow for more accurate interpretations from next-generation sequencing results. Molecular-based purity estimates using computational approaches require sequencing of tumors, which is both time-consuming and expensive.

Methods

Here we propose an approach, weakly-supervised purity (wsPurity), which can accurately quantify tumor purity within a digitally captured hematoxylin and eosin (H&E) stained histological slide, using several types of cancer from The Cancer Genome Atlas (TCGA) as a proof-of-concept.

Findings

Our model predicts …

Is The Phq-9 A Unidimensional Measure Of Depression? A 58,272-Participant Study, Renzo Bianchi, Jay Verkuilen, Sharon Toker, Irvin Sam Schonfeld, Markus Gerber, Elmar Brähler, Kurt Kroenke

Publications and Research

The PHQ-9 has become a measure of reference in depression research and clinical practice. However, the issue of the PHQ-9’s unidimensionality has not been fully elucidated, and the usability of the PHQ-9’s total score requires clarification. In this study, we examined the dimensionality, scalability, and monotonicity properties of the PHQ-9 as well as the scale’s total-score reliability. We did so based on exploratory structural equation modeling (ESEM) bifactor analysis and Mokken scale analysis (MSA). We relied on a total of 58,272 participants (63% female; Mage = 43, SDage = 13) from 29 samples involving seven different countries (e.g., Germany, the …

Correlations Between The Rotations And Magnetospheres Of The Terrestrial Planets And The Sun's Formation In Our Solar System, Fred J. Cadieu

Publications and Research

Correlations between the rotations of the terrestrial planets in our solar system and the magnetic field of the Sun have been previously noted. These correlations account for the opposite rotation of Venus as a result of the magnetic field of the Sun being dragged across the conducting core of Venus. Currently the Sun’s magnetic field is not sufficiently strong to account for the proposed correlations. But recently meteorite paleomagnetism measurements have indicated that during the Sun’s formation the magnetic field of the Sun was of sufficient strength to have resulted in the observed correlations. As a part of these correlations …

The Personal Papers Of American Sailors, 1890s–1940s, Annie E. Tummino

Publications and Research

Personal papers in the archives at Maritime College, State University of New York, document the lives of alumni from the school’s founding in 1874 through the early decades of the 20th century. Journals, diaries, memoirs, and reminiscences located in these collections provide evidence of what it was like to work on a ship, far from home, travelling to foreign lands. In this article, I explore first-hand accounts of maritime life by Van Horne Morris, my maternal grandfather and a 1938 graduate of the Massachusetts Nautical School (now known as Massachusetts Maritime Academy), and several alumni of the New York Nautical …

Challenges In Migrating Imperative Deep Learning Programs To Graph Execution: An Empirical Study, Tatiana Castro Vélez, Raffi Khatchadourian, Mehdi Bagherzadeh, Anita Raja

Publications and Research

Efficiency is essential to support responsiveness w.r.t. ever-growing datasets, especially for Deep Learning (DL) systems. DL frameworks have traditionally embraced deferred execution-style DL code that supports symbolic, graph-based Deep Neural Network (DNN) computation. While scalable, such development tends to produce DL code that is error-prone, non-intuitive, and difficult to debug. Consequently, more natural, less error-prone imperative DL frameworks encouraging eager execution have emerged at the expense of run-time performance. While hybrid approaches aim for the "best of both worlds," the challenges in applying them in the real world are largely unknown. We conduct a data-driven analysis of challenges—and resultant bugs—involved …

Challenges In Migrating Imperative Deep Learning Programs To Graph Execution: An Empirical Study, Tatiana Castro Vélez, Raffi Khatchadourian, Mehdi Bagherzadeh, Anita Raja

Publications and Research

Efficiency is essential to support responsiveness w.r.t. ever-growing datasets, especially for Deep Learning (DL) systems. DL frameworks have traditionally embraced deferred execution-style DL code that supports symbolic, graph-based Deep Neural Network (DNN) computation. While scalable, such development tends to produce DL code that is error-prone, non-intuitive, and difficult to debug. Consequently, more natural, less error-prone imperative DL frameworks encouraging eager execution have emerged at the expense of run-time performance. While hybrid approaches aim for the "best of both worlds," the challenges in applying them in the real world are largely unknown. We conduct a data-driven analysis of challenges—and resultant bugs—involved …

A Tool For Rejuvenating Feature Logging Levels Via Git Histories And Degree Of Interest, Yiming Tang, Allan Spektor, Raffi Khatchadourian, Mehdi Bagherzadeh

Publications and Research

Logging is a significant programming practice. Due to the highly transactional nature of modern software applications, a massive amount of logs are generated every day, which may overwhelm developers. Logging information overload can be dangerous to software applications. Using log levels, developers can print the useful information while hiding the verbose logs during software runtime. As software evolves, the log levels of logging statements associated with the surrounding software feature implementation may also need to be altered. Maintaining log levels necessitates a significant amount of manual effort. In this paper, we demonstrate an automated approach that can rejuvenate feature log …

Recent Advances In Bone Research 2022 Edition, Jean-Philippe Berteau, Laurent Pujo-Menjouet

Publications and Research

More and more scientific and engineering applications in bone research make pivotal advances in treating patients with orthopedics issues. Hence, bone research in the 21st century combines, inter alia, biology, chemistry, mathematics, and mechanics with complementary characteristics that help a holistic approach to bone-related pathologies. Nowadays, it is hard to connect new evidence when jargoning and money remain two significant obstacles to sharing knowledge. “Recent Advances In Bone Research” is a free book – no money involved at any stage - that combines the most recent efforts in bone research from several experts with different backgrounds, every expert seeks to …

Effectiveness And Safety Of Oral Anticoagulants In Non-Valvular Atrial Fibrillation Patients With Prior Bleeding Events: A Retrospective Analysis Of Administrative Claims Databases, G. Y. H. Lip, Allison V. Keshishian, Amiee Kang, Xuemei Luo, Nipun Atreja, Yan Zhang, Patricia Schuler, Jenny Jiang, Huseyin Yuce, Steve Deitelzweig

Publications and Research

Introduction

There are a paucity of real-world data examining effectiveness and safety of non-vitamin K antagonist oral anticoagulants (NOACs) and warfarin in nonvalvular atrial fibrillation (NVAF) patients with prior bleeding.

Methods

This retrospective analysis included data from 5 insurance claims databases and included NVAF patients prescribed OACs with prior bleeding. One-to-one propensity score matching was conducted between NOACs and warfarin and between NOACs in each database. Cox proportional hazards models were used to evaluate the risk of stroke/systemic embolism (SE) and MB.

Results

A total of 244,563 patients (mean age 77; 50% female) with prior bleeding included 55,094 (22.5%) treated …

The Living Breakwaters Pdr Efforts: Conceptual Scheduling, Calvin O. Walters Jr.

Publications and Research

On October 29, 2012, Superstorm Sandy caused nearly $19 billion in damages in New York City including 69,000 residential units across the five boroughs. This disaster precipitated a post-disaster-rebuilding (PDR) project including roughly $4.2 billion in a Community Development Block Grant allocated towards PDR projects. A portion of the grant was used to construct a living breakwater in Tottenville, Staten Island, consisting of a resiliency approach to risk reduction through erosion prevention, wave energy attenuation, and enhancement of ecosystems and social resiliency to improve resistance to storms for the community of Tottenville. The ridges of each breakwater are designed with …

Lake Satellite Temperature Data Validation, Mamadou Balde, Pascal Kouogang

Publications and Research

In environmental remote sensing, satellite data isn't absolutely conclusive, for that reason, there is a natural need to verify the data acquired from the satellite. The most suitable tool to achieve such verification is on ground sensors that have the advantage of proximity. Addressing any possible discrepancies between the satellite data and the ground sensor data is sure to yield ways to come up with improvements of satellite band calibration and sensing capabilities. This research focused on correlating temperature data from the MODIS satellite with the data obtained from the In Situ sensor located in Lake Sunapee. Doing the latter …

An Analysis Of Non-Comparison Based Sorting Algorithms, Jacob M. Gomez, Edgar Aponte, Brad Isaacson

Publications and Research

Sorting algorithms put elements of a list into an order (e.g., numerical, alphabetical). Sorting is an important problem because a nontrivial percentage of all computing resources are devoted to sorting all kinds of lists. For our project, we implemented two non-comparison based sorting algorithms from pseudocode and compared them to various comparison based sorting algorithms. The two algorithms have their advantages and disadvantages as well as their unique features. We found that Radix Sort (which is a modified version of Counting Sort) was the most efficient of them all.

Remote Sensing & Land Surface Temperature From Satellite Observations, Isatu Jollah

Publications and Research

The Moderate Resolution Imaging Spectroradiometer (MODIS) instrument is designed and developed in 1995. • It is a critical instrument aboard Terra and Aqua satellites. Terra's orbit around the Earth is timed so that it crosses the equator from north to south in the morning, while Aqua crosses the equator from south to north in the afternoon. • Every 1 to 2 days, Terra MODIS and Aqua MODIS scan the entire Earth's surface, collecting data in groups of wavelengths. • In this research, a whole month of MODIS Land Surface Temperature data from both Aqua and Terra were explored and investigated.

Exploration Of Chemical Space With Partial Labeled Noisy Student Self‑Training And Self‑Supervised Graph Embedding, Yang Liu, Hansaim Lim, Lei Xie

Publications and Research

Background Drug discovery is time-consuming and costly. Machine learning, especially deep learning, shows great potential in quantitative structure–activity relationship (QSAR) modeling to accelerate drug discovery process and reduce its cost. A big challenge in developing robust and generalizable deep learning models for QSAR is the lack of a large amount of data with high-quality and balanced labels. To address this challenge, we developed a self-training method, Partially LAbeled Noisy Student (PLANS), and a novel self-supervised graph embedding, Graph-Isomorphism-Network Fingerprint (GINFP), for chemical compounds representations with substructure information using unlabeled data. The representations can be used for predicting chemical properties such …

Dissociative Excitation, Ionization, And Fragmentation Processes For Nitrogen, Oxygen, Methane, And Water Molecules By Electron Bombardment, M. Gochitashvili, R. Lomsazde, D. Kuparashvili, O. Taboridze, Roman Ya. Kezerashvili

Publications and Research

Electron–impact ionization and fragmentation of molecules are investigated by the chromatography mass-spectrometry device. While the excitation processes are investigated by an optical spectroscopy method. The spectral analysis is performed in the vacuum ultraviolet 50-130 nm spectral regions. The absolute value of the fragmentation cross-section in the dissociative ionization and excitation processes is determined. Measurements are performed in the electron energy range 25-120eV for ionization and 200-500eV for excitation processes respectively.

A Role For Myosin Ii Clusters And Membrane Energy In Cortex Rupture For Dictyostelium Discoideum, Emmanuel Asante-Asamani, Daniel Grange, Devarshi Rawal, Zully Santiago, John Loustau, Derrick Brazill

Publications and Research

Blebs, pressure driven protrusions of the cell membrane, facilitate the movement of eukaryotic cells such as the soil amoeba Dictyostelium discoideum , white blood cells and cancer cells. Blebs initiate when the cell membrane separates from the underlying cortex. A local rupture of the cortex, has been suggested as a mechanism by which blebs are initiated. However, much clarity is still needed about how cells inherently regulate rupture of the cor- tex in locations where blebs are expected to form. In this work, we examine the role of mem- brane energy and the motor protein myosin II (myosin) in facilitating …

Superfluidity Of Dipolar Excitons In A Double Layer Of Α -T3 With A Mass Term, Oleg L. Berman, Godfrey Gumbs, Gabriel P. Martins, Paula Fekete

Publications and Research

We predict Bose-Einstein condensation and superfluidity of dipolar excitons, formed by electron-hole pairs in spatially separated gapped hexagonal α − T3 (GHAT3) layers. In the α − T3 model, the AB-honeycomb lattice structure is supplemented with C atoms located at the centers of the hexagons in the lattice. We considered the α − T3 model in the presence of a mass term which opens a gap in the energy-dispersive spectrum. The gap opening mass term, caused by a weak magnetic field, plays the role of Zeeman splitting at low magnetic fields for this pseudospin-1 system. The band structure of GHAT3 …

The Solar-Electric Sail: Application To Interstellar Migration And Consequences For Seti, Gregory Matloff

Publications and Research

The Solar-Electric Sail accelerates by reflecting positively charged solar wind ions. If it is used to propel an interstellar migration mission, its interstellar cruise velocity relative to the home star cannot exceed the solar wind velocity. In an effort to analytically determine interstellar cruise velocity for a 107 kg generation ship, a constant solar wind velocity within the heliosphere of a Sun-like star of 600 km/s is assumed. The solar wind proton density at 1 AU is also considered constant at 10 protons per cubic centimeter. Solar wind density is assumed to decrease with the inverse square of solar distance. …

Sum Of Mobius Functions Over The Shifted Primes, Nelson Carella

Publications and Research

This article provides an asymptotic result for the summatory Mobius function ∑ p≤x μ(p + a) = O (x log−c x) over the shifted primes, where a ̸ = 0 is a fixed parameter, and c > 1 is a constant.

Early Pleistocene Large Mammals From Maka’Amitalu, Hadar, Lower Awash Valley, Ethiopia, John Rowan, Ignacio A. Lazagabaster, Christopher J. Campisano, Faysal Bibi, René Bobe, Jean-Renaud Boisserie, Stephen R. Frost, Tomas Getachew, Christopher C. Gilbert, Margaret E. Lewis, Sahleselasie Melaku, Eric Scott, Antoine Souron, Lars Werdelin, William H. Kimbel, Kaye E. Reed

Publications and Research

The Early Pleistocene was a critical time period in the evolution of eastern African mammal faunas, but fossil assemblages sampling this interval are poorly known from Ethiopia ’ s Afar Depression. Field work by the Hadar Research Project in the Busidima Formation exposures (~2.7 – 0.8 Ma) of Hadar in the lower Awash Valley, resulted in the recovery of an early Homo maxilla (A.L. 666-1) with associated stone tools and fauna from the Maka ’ amitalu basin in the 1990s. These assemblages are dated to ~2.35 Ma by the Bouroukie Tuff 3 (BKT-3). Continued work by the Hadar Research Project …