Digital Commons Network^™

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.

A Comparison Of Individual Learning And Social Learning In Zebrafish Through An Ethorobotics Approach, Yanpeng Yang, Romain J. G. Clément, Stefano Ghirlanda, Maurizio Porfiri

Publications and Research

Social learning is ubiquitous across the animal kingdom, where animals learn from group members about predators, foraging strategies, and so on. Despite its prevalence and adaptive benefits, our understanding of social learning is far from complete. Here, we study observational learning in zebrafish, a popular animal model in neuroscience. Toward fine control of experimental variables and high consistency across trials, we developed a novel robotics-based experimental test paradigm, in which a robotic replica demonstrated to live subjects the correct door to join a group of conspecifics. We performed two experimental conditions. In the individual training condition, subjects learned the correct …

Bioluminescent Flashes Drive Nighttime Schooling Behavior And Synchronized Swimming Dynamics In Flashlight Fish, David F. Gruber, Brennan T. Phillips, Rory O'Brien, Vivek Boominathan, Ashok Veeraraghavan, Ganesh Vasan, Peter O'Brien, Vincent A. Pieribone, John S. Sparks

Publications and Research

Schooling fishes, like flocking birds and swarming insects, display remarkable behavioral coordination. While over 25% of fish species exhibit schooling behavior, nighttime schooling has rarely been observed or reported. This is due to vision being the primary modality for schooling, which is corroborated by the fact that most fish schools disperse at critically low light levels. Here we report on a large aggregation of the bioluminescent flashlight fish Anomalops katoptron that exhibited nighttime schooling behavior during multiple moon phases, including the new moon. Data were recorded with a suite of low-light imaging devices, including a high-speed, high-resolution scientific complementary metal-oxide-semiconductor …

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.

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 …

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 …

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.

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 …

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 …

Concept Mapping As A Mechanism For Assessing Science Teachers’ Cross-Disciplinary Field-Based Learning, Joanna K. Garner, Avi Kaplan, Stephanie Hathcock, Bradley W. Bergey

Publications and Research

Two common goals of science teacher professional development (PD) are increased content knowledge (CK) and improved readiness to teach through inquiry. However, PD assessment challenges arise when the context is structured around inquiry-based, participant-driven learning, and when the content crosses scientific disciplines. This study extended the use of concept mapping as an assessment tool for examining changes in the content knowledge of 21 high school science teachers who participated in a field-based environmental science summer institute. The scoring rubric focused on documenting concepts, links, and map organization and scope in an attempt to capture development of cross- disciplinary knowledge in …

One-Year Research Experience For Associate’S Degree Students Impacts Graduation, Stem Retention, And Transfer Patterns, Ron Nerio, Althea Webber, Effie Maclachlan, David Lopatto, Avrom J. Caplan

Publications and Research

The CUNY Research Scholars Program (CRSP) provides a yearlong faculty-mentored research experience to associate’s degree students. The program takes place at all 10 associate’s degree–granting colleges within the City University of New York system. We report on a mixed-methods study of 500 students who participated in the program during its initial 3 years. Quantitative longitudinal assessments revealed that students who en-gaged in CRSP were more likely to be retained in a science, technology, engineering, and mathematics (STEM) discipline or to graduate with a STEM degree than their counterparts in a matched comparison group. Furthermore, students who participated in CRSP demon-strated …

Study Of Healthcare-Associated Infections And Multi-Drug Resistance In Brooklyn: An Integrative Approach, Liana Tsenova, Urmi Ghosh-Dastidar, Arnavaz Taraporevala, Pamela Brown, Aionga Pereira-Edwards

Publications and Research

One SENCER ideal is to connect science education and civic engagement by student learning through complex, unresolved public issues. Using this approach, we established a collaborative interdisciplinary project involving faculty and undergraduate students at NYC College of Technology. Over several semesters, students conducted literature search and discovered the complex factors contributing to the occurrence and transmission of healthcare-associated infections (HAIs). Using microbiology data from 15 hospitals in Brooklyn, NY, they applied statistical analyses, studied the antibiotic resistance, and developed a campaign to bring more awareness of this problem. The results of the project highlight the importance of immediate action in …

Education And Marriage Decisions Of Japanese Women And The Role Of The Equal Employment Opportunity Act, Linda N. Edwards, Takuya Hasebe, Tadashi Sakai

Publications and Research

The Japanese Equal Employment Opportunity Act (EEOA) of 1985 aimed to reduce gender discrimination in the labor market, especially for career-oriented jobs. This paper investigates whether this act had an unanticipated effect on women's marriage decisions. Using micro data from the Japanese Panel Survey of Consumers, we model women's interrelated decisions on university education and whether to marry, focusing on whether women have married by age 32. Our results show a negative relationship between university education and marriage that is much greater for post-EEOA cohorts of women than for pre-EEOA cohorts, consistent with our hypothesis that the enhanced career opportunities …

In Search Of China’S First Library: Materials, Housing And Arrangement, Junli Diao

Publications and Research

Historically, the origin of libraries has an intimate association with written records supporting administrative or ritual functions at the palace or temple. This article attempts to discuss the possibility of the existence of China’s first library in the Shang dynasty (c.1570-1045 BCE) during the beginning of the formative period of Chinese civilization. The article analyzes and synthesizes both paleographical and archaeological evidence from the perspective of available materials, houses, and arrangement, which answers the questions of what the books were made of, where they were stored, and how they were arranged. The article ends with a conclusion that there is …

Board 121: Development Of A Create-A-Lego-Engineer Activity To Examine Students’ Engineering Identity, Kelli Paul, Euisuk Sung, Adam V. Maltese, Karen Miel, Merredith D. Portsmore

Publications and Research

This paper describes the development of a Create-a-Lego-Engineer (CALE) activity which was created as an alternative to the Draw-a-Scientist (DAST) and Draw-an-Engineer Tests (DAET). While the DAST and DAET examine students’ (mis)conceptions of scientists and engineers, they provide limited information about whether students can envision themselves as scientists or engineers now or in the future. We drew from the Lego Serious Play (LSP) method which is grounded on the premise that hands-on learning results in a deeper understanding of the world and oneself in it. The LSP method is a process used to enhance innovation and business development, and it …

Senior Design Case Study: Application Of System Engineering Concepts In The Design Of A Router, Angran Xiao, Rafaela Alba, Ozlem Yasar, Andy S. Zhang, Gaffar Gailani

Publications and Research

System engineering (SE) is a multidisciplinary approach for the design, management, and realization of a complex system. In product development, SE is utilized on structuring a product development process into simple and collaborative activities that proceed throughout the entire product life-cycle, while at the same time, supporting engineers’ decision making. Project based engineering design classes are suitable for undergraduate students to study and practice the concepts of SE while solving real-world design problems. In this paper, we document the product development process, especially the structured design methodologies used in an undergraduate Senior Design project. Student learning outcomes are assessed and …

Board 120: Development Of An Engineering Identity And Career Aspirations Survey For Use With Elementary Students, Kelli Paul, Adam V. Maltese, Karen Miel, Merredith D. Portsmore, Euisuk Sung

Publications and Research

Interest in science, technology, engineering, and mathematics (STEM) begins as early as elementary and middle school. As youth enter adolescence, they begin to shape their personal identities and start making decisions about who they are and could be in the future. Students form their career aspirations and interests related to STEM in elementary school, long before they choose STEM coursework in high school or college. Much of the literature examines either science or STEM identity and career aspirations without separating out individual sub-disciplines. Therefore, the purpose of this paper is to describe the development of a survey instrument to specifically …

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.

A Qualitative Analysis To Identify The Elements That Support Department Level Change In The Life Sciences: The Pulse Vision & Change Recognition Program, Mary Peteroy-Kelly, Loretta Brancaccio-Taras, Judy Awong-Taylor, Teresa Balser, Thomas Jack, Sara Lindsay, Kate Marley, Sandra Romano, J. Akif Uzman, Pamela Pape-Lindstrom

Publications and Research

The 2011 report, Vision and Change in Undergraduate Biology Education: A Call to Action, provided the impetus to mobilize the undergraduate life sciences education community to affect change in order to enhance the educational experiences of life sciences majors. The work of the appointed Partnership for Undergraduate Life Sciences Education (PULSE) Vision and Change (V&C) Leadership Fellows has focused on the development of programs and resources to support departmental change. In this report, we present a qualitative assessment of several documents generated from the PULSE V&C Leadership Fellow Recognition Team. The Recognition Team developed two initiatives to provide …

Readability Of Online-Patient Based Information On Bariatric Surgery, Zoë Meleo-Erwin, Corey Basch, Joseph Fera, Danna Ethan, Philip Garcia

Publications and Research

Background: Web-based patient education literature has been shown to be written at reading levels far above what is recommended. Little is known about the overall readability of current internet-based bariatric surgery information. The purpose of this study was to assess the readability of current bariatric material on the internet.

Methods: The term “weight loss surgery” was searched using the Chrome browser on the first 15 pages of URLs that appeared with content written in English. Using five readability measures, scores were generated using Readable.io for written content on a sample of 96 websites. Scores were sorted into the readability categories …

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.