Physical Sciences and Mathematics Commons^™

Small Molecule Modulation Of Microbiota: A Systems Pharmacology Perspective, Qiao Liu, Bohyun Lee, Lei Xie

Publications and Research

Background

Microbes are associated with many human diseases and influence drug efficacy. Small-molecule drugs may revolutionize biomedicine by fine-tuning the microbiota on the basis of individual patient microbiome signatures. However, emerging endeavors in small-molecule microbiome drug discovery continue to follow a conventional “one-drug-one-target-one-disease” process. A systematic pharmacology approach that would suppress multiple interacting pathogenic species in the microbiome, could offer an attractive alternative solution.

Results

We construct a disease-centric signed microbe–microbe interaction network using curated microbe metabolite information and their effects on host. We develop a Signed Random Walk with Restart algorithm for the accurate prediction of effect of microbes …

Toward Informatics-Enabled Preparedness For Natural Hazards To Minimize Health Impacts Of Climate Change, Jimmy Phuong, Naomi O. Riches, Luca Calzoni, Gora Datta, Deborah Duran, Asiyah Yu Lin, Ramesh P. Singh, Anthony E. Solomonides, Noreen Y. Whysel, Ramakanth Kavuluru

Publications and Research

Natural hazards (NHs) associated with climate change have been increasing in frequency and intensity. These acute events impact humans both directly and through their effects on social and environmental determinants of health. Rather than relying on a fully reactive incident response disposition, it is crucial to ramp up preparedness initiatives for worsening case scenarios. In this perspective, we review the landscape of NH effects for human health and explore the potential of health informatics to address associated challenges, specifically from a preparedness angle. We outline important components in a health informatics agenda for hazard preparedness involving hazard-disease associations, social determinants …

Markovnikov Alcohols Via Epoxide Hydroboration By Molecular Alkali Metal Catalysts, Guoqi Zhang, Haisu Zeng, Shengping Zheng, Michelle C. Neary, Los Alamos National Laboratory

Publications and Research

Summary

How Many Mutex Bugs Can A Simple Analysis Find In Go Programs?, Fumi Takeuchi, Hidehiko Masuhara, Raffi Khatchadourian, Youyou Cong, Keisuke Ishibashi

Publications and Research

In open-source software, it is known that there are many concurrency bugs. A previous study in Go revealed that a considerable number of such bugs are simple (for example, 9% of the bugs are the ones that forget to unlock a mutex,) through a manual program investigation. This paper tries to detect such bugs by applying a simple analysis to see how far such a tool can match the manual analysis. We built a simple intraprocedural control flow analysis in Go, and evaluated its performance concerning the open source programs with concurrency bugs reported in the previous study. Consequently, as …

Generalization Of Bi-Canonical Degrees, Joseph Brennan, Laura Ghezzi, Jooyoun Hong, Wolmer Vasconcelos

Publications and Research

We discuss invariants of Cohen-Macaulay local rings that admit a canonical module ω. Attached to each such ring R, when ω is an ideal, there are integers–the type of R, the reduction number of ω–that provide valuable metrics to express the deviation of R from being a Gorenstein ring. In (Ghezzi et al. in JMS 589:506–528, 2017) and (Ghezzi et al. in JMS 571:55–74, 2021) we enlarged this list with the canonical degree and the bi-canonical degree. In this work we extend the bi-canonical degree to rings where ω is not necessarily an ideal. We also discuss generalizations to rings …

Asian Hate Speech Detection On Twitter During Covid-19, Amir Toliyat, Sarah Ita Levitan, Zeng Peng, Ronak Etemadpour

Publications and Research

Coronavirus disease 2019 (COVID-19) started in Wuhan, China, in late 2019, and after being utterly contagious in Asian countries, it rapidly spread to other countries. This disease caused governments worldwide to declare a public health crisis with severe measures taken to reduce the speed of the spread of the disease. This pandemic affected the lives of millions of people. Many citizens that lost their loved ones and jobs experienced a wide range of emotions, such as disbelief, shock, concerns about health, fear about food supplies, anxiety, and panic. All of the aforementioned phenomena led to the spread of racism and …

A Decade Review Of Disease Surveillance Research Trends In The International Journal Of Health Geographics (2009 To 2018), Rose Jimenez, Paradorn Wongchanapai

Publications and Research

The field of health geographics is rapidly growing in its methods and epistemologies. This is a review of the open-source journal International Journal of Health Geographics, and the trends in disease surveillance over ten years (2009-2018). Drawing from research review methodologies, we wrote a Python script to quantify research trends within the field of geographic disease surveillance, finding many articles focusing on population health, techniques of GIS, qualitative techniques, and geospatial technology for health monitoring. This was foundational in conducting an in-depth qualitative lexical analysis of article content and epistemologies. Overall, we concluded that over the time period, the …

The 'Quantal Newtonian' First Law: A Complementary Perspective To The Stationary-State Quantum Theory Of Electrons, Viraht Sahni

Publications and Research

A complementary perspective to the Göttingen-Copenhagen interpretation of stationary-state quantum theory of electrons in an electromagnetic field is described. The perspective, derived from Schrödinger-Pauli theory, is that of the individual electron via its equation of motion or ‘Quantal Newtonian’ First Law. The Law is in terms of ‘classical’ fields experienced by each electron: the sum of the external and internal fields vanishes. The external field is a sum of the electrostatic and Lorentz fields. The internal field is a sum of fields’ representative of Pauli and Coulomb correlations; kinetic effects; electron density; and internal magnetic component. The energy is obtained …

Arrayed Waveguide Lens For Beam Steering, Mostafa Honari-Latifpour, Ali Binaie, Mohammad Amin Eftekhar, Nicholas Madamopoulos, Mohammad-Ali Miri

Publications and Research

Integrated planar lenses are critical components for analog optical information processing that enable a wide range of applications including beam steering. Conventional planar lenses require gradient index control which makes their on-chip realization challenging. Here, we introduce a new approach for beam steering by designing an array of coupled waveguides with segmented tails that allow for simultaneously achieving planar lensing and off-chip radiation. The proposed arrayed waveguide lens is built on engineering the evanescent coupling between adjacent channels to realize a photonic lattice with an equi-distant ladder of propagation constants that emulates the continuous parabolic index profile. Through coupled-mode analysis …

Code Cyber: A Curated Collection Of Cybersecurity Career Learning And Preparation Resources, Kazi Tasin, Ethan Pruzhansky, Jason Lin, Tanvir Rahman, Patrick J. Slattery

Publications and Research

Since we are living in a digital age, the need to protect ourselves and those who are vulnerable to cyber-attacks is paramount to prevent cyber attacks that steal information such as banking accounts and important sensitive information.

Our research team extensively investigated the five aspects of cybersecurity such as identity, protection, detection, and response. By conducting various interviews with cybersecurity professionals, we gathered information about these five aspects for example security intelligence or security operations and response, (thread hunting, response orchestration) identity access management, (identity management, and data protection), and risks (risk perspective). Our main goal is to look into …

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 …

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 …

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 …

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 …

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 …

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.

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 …

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.

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.