Physical Sciences and Mathematics Commons^™

Integrating Ligand-Receptor Interactions And In Vitro Evolution For Streamlined Discovery Of Artificial Nucleic Acid Ligands, Hasan E. Zumrut, Sana Batool, Kimon V. Argyropoulos, Nicole Williams, Roksana Azad, Prabodhika R. Mallikaratchy

Publications and Research

To discover DNA ligands against a predetermined receptor protein complex, we introduce a comprehensive version of ligand-guided selection (LIGS). LIGS is, itself, a variant of systematic evolution of ligands by exponential enrichment (SELEX). Herein, we have optimized LIGS to identify higher affinity aptamers with high specificity. In addition, we demonstrate the expandability of LIGS by performing specific aptamer elution at 25C, utilizing multiple monoclonal antibodies (mAbs) against cultured cells and primary cells obtained from human donors expressing the same receptor. Eluted LIGS libraries obtained through Illumina high-throughput (HT) DNA sequencing were analyzed by bioinformatics tools to discover five DNA aptamers …

Amazon Alexa + Linked Open Data: Theorizing Concerning Relationships Between (Surveillant) Smart-Home Voice Assistants And Linked Open Data, Michelle Nitto

Publications and Research

No abstract provided.

Deep Machine Learning Techniques For The Detection And Classification Of Sperm Whale Bioacoustics, Peter C. Bermant, Michael M. Bronstein, Robert J. Wood, Shane Gero, David F. Gruber

Publications and Research

We implemented Machine Learning (ML) techniques to advance the study of sperm whale (Physeter macrocephalus) bioacoustics. This entailed employing Convolutional Neural Networks (CNNs) to construct an echolocation click detector designed to classify spectrograms generated from sperm whale acoustic data according to the presence or absence of a click. The click detector achieved 99.5% accuracy in classifying 650 spectrograms. The successful application of CNNs to clicks reveals the potential of future studies to train CNN-based architectures to extract finer-scale details from cetacean spectrograms. Long short-term memory and gated recurrent unit recurrent neural networks were trained to perform classification tasks, including (1) …

Going Big: A Large-Scale Study On What Big Data Developers Ask, Mehdi Bagherzadeh, Raffi Khatchadourian

Publications and Research

Software developers are increasingly required to write big data code. However, they find big data software development challenging. To help these developers it is necessary to understand big data topics that they are interested in and the difficulty of finding answers for questions in these topics. In this work, we conduct a large-scale study on Stackoverflow to understand the interest and difficulties of big data developers. To conduct the study, we develop a set of big data tags to extract big data posts from Stackoverflow; use topic modeling to group these posts into big data topics; group similar topics into …

Yields Of Weakly Bound Light Nuclei As A Probe Of The Statistical Hadronization Model, Yiming Cai, Thomas D. Cohen, Boris A. Gelman, Yukari Yamauchi

Publications and Research

The statistical hadronization model successfully describes the yields of hadrons and light nuclei from central heavy-ion collisions over a wide range of energies. It is a simple and efficient phenomenological framework in which the relative yields for very high energy collisions are essentially determined by a single model parameter—the chemical freeze-out temperature. Recent measurements of yields of hadrons and light nuclei covering over nine orders of magnitudes from the ALICE collaboration at the Large Hadron Collider were described by the model with remarkable accuracy with a chemical freeze-out temperature of 156.5 ± 1.5 MeV. A key physical question is whether …

Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman

Publications and Research

Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUDE). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular …

Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman

Publications and Research

Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUDE). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular …

A Note On Distance-Based Entropy Of Dendrimers, Modjtaba Ghorbani, Matthias Dehmer, Samaneh Zangi, Abbe Mowshowitz, Frank Emmert-Streib

Publications and Research

This paper introduces a variant of entropy measures based on vertex eccentricity and applies it to all graphs representing the isomers of octane. Taking into account the vertex degree as well (degree-ecc-entropy), we find a good correlation with the acentric factor of octane isomers. In particular, we compute the degree-ecc-entropy for three classes of dendrimer graphs.

Master Integrals For The Two-Loop, Non-Planar Qcd Corrections To Top-Quark Pair Production In The Quark-Annihilation Channel, Matteo Becchetti, Roberto Bonciani, Valerio Casconi, Andrea Ferroglia, Simone Lavacca, Andreas Von Manteuffel

Publications and Research

We present the analytic calculation of the Master Integrals for the two-loop, non-planar topologies that enter the calculation of the amplitude for top-quark pair hadroproduction in the quark-annihilation channel. Using the method of differential equations, we expand the integrals in powers of the dimensional regulator ε and determine the expansion coefficients in terms of generalized harmonic polylogarithms of two dimensionless variables through to weight four.

Synthesis And Evaluations Of “1,4-Triazolyl Combretacoumarins” And Desmethoxy Analogs, Tashrique A. Khandaker, Jessica D. Hess, Renato Aguilera, Graciela Andrei, Robert Snoeck, Dominique Schols, Padmanava Pradhan, Mahesh K. Lakshman

Publications and Research

1,4-Triazolyl combretacoumarins have been prepared by linking the trimethoxyarene unit of combretastatin A4 with coumarins, via a 1,2,3-triazole. For this, 4-azidocoumarins were accessed by a sequential two-step, one-pot reaction of 4-hydroxycoumarins with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP), followed by reaction with NaN₃. In the reaction with BOP, a coumarin-derived phosphonium ion intermediate seems to form, leading to an O⁴-(benzotriazolyl)coumarin derivative. For the CuAAC reaction of azidocoumarins with 5-ethynyl-1,2,3-trimethoxybenzene, catalytic [(MeCN)₄Cu]PF₆ in CH₂Cl₂/MeOH with 2,6-lutidine, at 50 ^oC, was suitable. The 4-azidocoumarins were less reactive as compared to PhN₃ and …

Top-Quark Pair Hadroproduction In Association With A Heavy Boson At Nlo+Nnll Including Ew Corrections, Alessandro Broggio, Andrea Ferroglia, Rikkert Frederix, Davide Pagani, Benjamin D. Pecjak, Ioannis Tsinikos

Publications and Research

This work studies the associated production of a top-quark pair with a W, Z, or Higgs boson at the LHC. Predictions for the total cross sections as well as for several differential distributions of the massive particles in the final state are provided. These predictions, valid for the LHC operating at 13 TeV, include without any approximation all the NLO electroweak and QCD contributions of O (α^sα^j+1) with i + j = 2, 3. In addition, the predictions presented here improve upon the NLO QCD results by adding the effects of soft gluon emission corrections resummed …

An Optimized Encoding Algorithm For Systematic Polar Codes, Xiumin Wang, Zhihong Zhang, Jun Li, Yu Wang, Haiyan Cao, Zhengquan Li, Liang Shan

Publications and Research

Many different encoding algorithms for systematic polar codes (SPC) have been introduced since SPC was proposed in 2011. However, the number of the computing units of exclusive OR (XOR) has not been optimized yet. According to an iterative property of the generator matrix and particular lower triangular structure of the matrix, we propose an optimized encoding algorithm (OEA) of SPC that can reduce the number of XOR computing units compared with existing non-recursive algorithms. We also prove that this property of the generator matrix could extend to different code lengths and rates of the polar codes. Through the matrix segmentation …

Rocketry And Observability Predictions For Cubesat, Juliano A. Everett

Publications and Research

Estimating the visibility of Sunlight reflected by the holographic retro-reflector of Cubesat Alpha, and to convert this to star apparent magnitude to learn more about the visibility of these sails through reflected sunlight, to in turn determine if glints of these holograms are visible by terrestrial observers.

How Do Anticipated And Self Regulations And Information Sourcing Openness Drive Firms To Implement Eco-Innovation? Evidence From Korean Manufacturing Firms, Cheon Yu, Junghoon Park, Yun Seop Hwang

Publications and Research

Building upon institutional theory and the concept of openness to external sources in terms of breadth and depth, this study investigates the following three understudied drivers of eco-innovation in terms of external and internal factors: Anticipated regulation and self-regulation as external drivers, and information sourcing openness comprised of breadth and importance as internal drivers. Toward this end, this study employs a sample of 1824 Korean manufacturing firms collected from the Korean Innovation Survey 2010, which is compatible with the Oslo Manual and the Eurostat Community Innovation Survey (CIS). The current research adopts a multivariate probit model for the nine binary …

An Early Modern Human Outside Africa, Eric Delson

Publications and Research

Analysis of two fossils from a Greek cave has shed light on early hominins in Eurasia. One fossil is the earliest known specimen of Homo sapiens found outside Africa; the other is a Neanderthal who lived 40,000 years later.

Safe Automated Refactoring For Intelligent Parallelization Of Java 8 Streams, Raffi Khatchadourian, Yiming Tang, Mehdi Bagherzadeh, Syed Ahmed

Publications and Research

Streaming APIs are becoming more pervasive in mainstream Object-Oriented programming languages and platforms. For example, the Stream API introduced in Java 8 allows for functional-like, MapReduce-style operations in processing both finite, e.g., collections, and infinite data structures. However, using this API efficiently involves subtle considerations such as determining when it is best for stream operations to run in parallel, when running operations in parallel can be less efficient, and when it is safe to run in parallel due to possible lambda expression side-effects. Also, streams may not run all operations in parallel depending on particular collectors used in reductions. In …

Unconventional Anticancer Metallodrugs And Strategies To Improve Their Pharmacological Profile, Maria Contel

Publications and Research

No abstract provided.

A Molecular Reconstruction Approach To Sitebased 3d-Rism And Comparison To Gist Hydration Thermodynamic Maps In An Enzyme Active Site, Crystal Nguyen, Takeshi Yamazaki, Andriy Kovalenko, David A. Case, Michael K. Gilson, Tom Kurtzman, Tyler Luchko

Publications and Research

Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular dynamics simulations, recent developments in the 3D reference interaction site model (3D-RISM) theory allow many of the same quantities to be calculated in a fraction of the time. However, 3D-RISM produces atomic-site, rather than molecular, density distributions, which are difficult to extract physical meaning from. To overcome this difficulty, we introduce a method to reconstruct molecular density distributions from atomic site density distributions. Furthermore, …

Sickle Cell Disease Complications: Prevalence And Resource Utilization, Nirmish Shah, Menaka Bhor, Lin Xi, Jincy Paulose, Huseyin Yuce

Publications and Research

Objectives: This study evaluated the prevalence rate of vaso-occlusive crisis (VOC) episodes, rates of uncomplicated and complicated VOC episodes, and the primary reasons for emergency room (ER) visits and inpatient admissions for sickle cell disease (SCD) patients.

Methods: The Medicaid Analytic extracts database was used to identify adult SCD patients using claims from 01JUL2009-31DEC2012. The date of the first observed SCD claim was designated as the index date. Patients were required to have continuous medical and pharmacy benefits for .6 months baseline and .12 months follow-up period. Patient demographics, baseline clinical characteristics, the rate of uncomplicated and complicated VOC (VOC …

A Field Procedure To Screen Soil For Hazardous Lead, Franziska C. Landers, Anna Paltseva, Jennifer M. Sobolewski, Zhongqi Cheng, Tyler K. Ellis, Brian J. Mailloux, Alexander Van Geen

Publications and Research

Soils retain lead contamination from possible sources such as mining, smelting, battery recycling, waste incineration, leaded gasoline, and crumbling paint. Such contamination is often concentrated in toxic hot spots that need to be identified locally. To address this need, a simple field procedure was designed to screen soil for hazardous Pb for use by the general public. The procedure is a modification of the in vitro soil Pb extraction described by Drexler and Brattin (Hum. Ecol. Risk Assess. 2007, 13, 383) and EPA Method 1340, and uses a 0.4 M glycine solution at pH 1.5. A higher soil-to-solution ratio of …

Weaving The Dark Web: Legitimacy On Freenet, Tor, And I2p, John Schriner

Publications and Research

This is a book review of Robert W. Gehl's Weaving the Dark Web: Legitimacy on Freenet, Tor, and I2P (2018). The book explores these anonymity networks and the concept of legitimacy throughout. Using a multidisciplinary approach and interviews with network-builders and users, Gehl helps to demystify the dark web and critically examine these networks and technologies.

Safe Automated Refactoring For Intelligent Parallelization Of Java 8 Streams, Raffi Khatchadourian, Yiming Tang, Mehdi Bagherzadeh, Syed Ahmed

Publications and Research

Streaming APIs are becoming more pervasive in mainstream Object-Oriented programming languages. For example, the Stream API introduced in Java 8 allows for functional-like, MapReduce-style operations in processing both finite and infinite data structures. However, using this API efficiently involves subtle considerations like determining when it is best for stream operations to run in parallel, when running operations in parallel can be less efficient, and when it is safe to run in parallel due to possible lambda expression side-effects. In this paper, we present an automated refactoring approach that assists developers in writing efficient stream code in a semantics-preserving fashion. The …

On Properties Of Distance-Based Entropies On Fullerene Graphs, Modjtaba Ghorbani, Matthias Dehmer, Mina Rajabi-Parsa, Abbe Mowshowitz, Frank Emmert-Streib

Publications and Research

In this paper, we study several distance-based entropy measures on fullerene graphs. These include the topological information content of a graph I_a(G), a degree-based entropy measure, the eccentric-entropy If_s(G), the Hosoya entropy H(G) and, finally, the radial centric information entropy H_ecc. We compare these measures on two infinite classes of fullerene graphs denoted by A_12n+4 and B_12n+6. We have chosen these measures as they are easily computable and capture meaningful graph properties. To demonstrate the utility of these measures, we investigate the Pearson correlation between them on the fullerene graphs.

Development Of Digital Bathymetry Maps For Lakes Azuei And Enriquillo Using Sonar And Remote Sensing Techniques, Michael Piasecki, Mahrokh Moknatian, Fred Moshary, Jorge Gonzalez

Publications and Research

This article presents an improved algorithm for optimization and development of a digital bathymetric model (DBM) for Lake Azuei (LA) (Haiti) and Lake Enriquillo (LE) (Dominican Republic) using the ANUDEM method. Both sonar data and contour lines of the lakes’ layout extracted using Landsat imagery were compiled for bathymetry development. We show that the performance of the ANUDEM method was strongly dependent on the density and irregularity of the spatial distribution of the data. Changing the resolution of the output grids and deriving auxiliary topographically corrected contours improved the ANUDEM performance and minimized the systematic errors of the method. Statistical …

Understanding Water Consumption And Energy Trends In New York City, Wen Yong Huang, Johann Thiel

Publications and Research

In this study, we will be using the NYC Open Data website to examine publicly available data sets on water and energy consumption in New York City. In particular, we will use various scientific programming and machine learning modules in Python to analyze and visualize trends in water and energy usage within the five boroughs.

Titanium Dioxide Sensitized With Porphyrin Dye As A Photocatalyst For The Degradation Of Water Pollutants, Kevin Reyes, Ivana Jovanovic

Publications and Research

TiO2 was sensitized with a porphyrin, Tetra(4-carboxyphenyl) porphyrin(TCPP) and used as photocatalyst under visible light for degradation of aqueous solutions of methylene blue (MB) dye. The quantification of the degradation of MB was assessed by UV-Vis spectroscopy. The results of this procedure showed the decrease in concentration of MB over time when reaction is exposed to visible light. The TiO2-TCPP complex was tested as well for the recovery of metals from the AgNO3 aqueous solution. The reduction of silver cations to silver metal was observed through formation of black precipitate.

The Dionysus Project: Classifying & Monitoring Vineyards With Satellite Remote Sensing & Image Analysis, Evelin Perez-Flores, Nicole Flores, Rachel Zinberg, Dionne Huston, Aaron Davitt, Kyle Mcdonald

Publications and Research

Climate change is expected to impact the wine industry by shifting suitable growing regions away from established regions and increasing the demand for freshwater supplies to maintain vineyard health. This creates challenges for maintaining vineyards since the grapevines need to be appropriately stressed to produce quality grapes for quality wine. This requires precision management of freshwater application and canopy management to produce a grape that has the appropriate concentration of flavors and sugars. Vineyards in the U.S. are typically monitored by vineyard managers at the large scale, lacking the resolution needed to identify grapevine growth at the subfield level. Vineyard …

Understanding The Impact Of Peer-Led Workshops On Student Learning, Afolabi Ibitoye, Nadia Kennedy, Armando Cosme

Publications and Research

As students we often wonder why some subjects are easy to understand and requires not much effort in terms of re-reading the material, for us to grasp what it entails. One subject seems to remain elusive and uneasy for a vast majority of learners at all levels of education; that subject is Mathematics, it is one subject that most learners finds difficult even after doubling the amount of time spent on studying the material. My intention is to explore ways to make Mathematics easier for other students using feedback from students enrolled in NSF mathematics peer leading workshops, and use …

A Comparative Study Of Incidence Of Domestic Violence Between Immigrant And Non-Immigrant Women In The United States Of America, Nadia A. Gordon, Urmi Ghosh-Dastidar, Janet Liou-Mark, Shamita Dasgupta

Publications and Research

Immigrant women in the USA come from various socio-economic, cultural, and religious backgrounds. Some of these women suffer from domestic violence; however, due to their strict cultural or social structure, they often stay quiet and rarely report these incidents to the authorities. Additionally, since these immigrant women face more challenges than their non-immigrant peers, they are more reluctant or unlikely to leave their abusive partners. An analysis was completed using published data as an attempt to establish if any statistically significant differences exist between reported incidences among immigrant women and non-immigrant women. A chi-square analysis (χ² = 14.53; p-value …

Simulation As A Predictor In Probability, Xiaona Zhou

Publications and Research

In this study, we simulate bivariate normal data. We gain intuition about the bivariate normal distribution by comparing the generated data to the associated bivariate normal density surface. We also get results about covariance and correlation. We will use tools from linear algebra to discuss transformations of random normal vectors, and the use of contours.