Digital Commons Network^™

Exploration Of Dark Chemical Genomics Space Via Portal Learning: Applied To Targeting The Undruggable Genome And Covid-19 Anti-Infective Polypharmacology, Tian Cai, Li Xie, Muge Chen, Yang Liu, Di He, Shuo Zhang, Cameron Mura, Philip Boume, Lei Xie

Publications and Research

Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental hurdle when applied to unseen data with distributions that differ from previously observed ones—a common dilemma in scientific inquiry. We have developed a new deep learning framework, called Portal Learning , to explore dark chemical and biological space. Three key, novel components of our approach include: (i) end-to-end, step-wise transfer learning, in recognition of biology’s sequence-structure-function paradigm, (ii) out-of-cluster meta-learning, and (iii) stress model selection. Portal Learning provides a practical solution to the out-of-distribution (OOD) …

Role Played By Edge-Defects In The Optical Properties Of Armchair Graphene Nanoribbons, Thi-Nga Do, Godfrey Gumbs, Danhong Huang, Bui D. Hoi, Po-Hsin Shih

Publications and Research

We explore the implementation of specific optical properties of armchair graphene nanoribbons (AGNRs) through edge-defect manipulation. This technique employs the tight-binding model in conjunction with the calculated absorption spectral function. Modification of the edge states gives rise to the diverse electronic structures with striking changes in the band gap and special flat bands at low energy. The optical-absorption spectra exhibit unique excitation peaks, and they strongly depend on the type and period of the edge extension. Remarkably, there exist the unusual transition channels associated with the flat bands for selected edge-modified systems. We discovered the special rule governing how the …

The Aesthetic Legacy Of Evolution: The History Of The Arts As A Window Into Human Nature, Aaron Kozbelt

Publications and Research

No abstract provided.

Peer-Led Team Learning In Mathematics: An Effort To Address Diversity And Inclusion Through Learning And Leadership, Janet Liou-Mark, Melanie L. Villatoro, Ariane Masuda, Malika Ikramova, Farjana Shati, Julia Rivera, Victor Lee

Publications and Research

The Peer-Led Team Learning (PLTL) model has shown to be an effective instructional method to support females, underrepresented minorities, and first-generation students in Science, Technology, Engineering, and Mathematics (STEM). The collaborative problem-solving setting, led by a peer leader, fosters learning that engages all the students. There are six critical components that are vital to the PLTL model: 1) The PLTL Workshop is integral to the course; 2) Faculty is actively involved; 3) Peer Leaders are well trained; 4) The PLTL Workshop modules are challenging; 5) PLTL workshops are allocated time and space; and 6) There is institutional support. City Tech …

Guidance For Management Of Free-Roaming Community Cats: A Bioeconomic Analysis, Valeria A. Benka, John D. Boone, Philip S. Miller, Joyce R. Briggs, Aaron M. Anderson, Christopher Slootmaker, Margaret Slater, Julie K. Levy, Felicia B. Nutter, Stephen Zawistowski

Publications and Research

Objectives This study used computer simulation modeling to estimate and compare costs of different free-roaming cat (FRC) management options (lethal and non-lethal removal, trap–neuter–return, combinations of these options and no action) and their ability to reduce FRC population abundance in open demographic settings. The findings provide a resource for selecting management approaches that are well matched for specific communities, goals and timelines, and they represent use of best available science to address FRC issues.

Methods Multiple FRC management approaches were simulated at varying intensities using a stochastic individual- based model in the software package Vortex. Itemized costs were obtained from …

Me3al-Mediated Domino Nucleophilic Addition/Intramolecular Cyclisation Of 2-(2-Oxo-2-Phenylethyl)Benzonitriles With Amines; A Convenient Approach For The Synthesis Of Substituted 1-Aminoisoquinolines, Krishna M. S. Adusumalli, Lakshmi N.S. Konidena, Hima B. Gandham, Krishnaiah Kumari, Krishan R. Valluru, Satya K.R. Nidasanametla, Venkateswara R. Battula, Hari K. Namballa

Publications and Research

A simple and efficient protocol for the construction of 1-aminoisoquinolines was achieved by treating 2-(2-oxo-2- phenylethyl)benzonitriles with amines in the presence of Me 3 Al. The reaction proceeds via a domino nucleophilic addition with subsequent intramolecular cyclisation. This method provides a wide variety of substituted 1-aminoisoquinolines with good func- tional group tolerance. Furthermore, the synthetic utility of this protocol was demonstrated in the successful synthesis of the anti- tumor agent CWJ-a-5 in gram scale.

Treatment Selection Using Prototyping In Latent-Space With Application To Depression Treatment, Akiva Kleinerman, Ariel Rosenfeld, David Benrimoh, Robert Fratila, Caitrin Armstrong, Joseph Mehltretter, Eliyahu Shneider, Amit Yaniv-Rosenfeld, Jordan Karp, Charles F. Reynolds, Gustavo Turecki, Adam Kapelner

Publications and Research

Machine-assisted treatment selection commonly follows one of two paradigms: a fully personalized paradigm which ignores any possible clustering of patients; or a sub-grouping paradigm which ignores personal differences within the identified groups. While both paradigms have shown promising results, each of them suffers from important limitations. In this article, we propose a novel deep learning-based treatment selection approach that is shown to strike a balance between the two paradigms using latent-space prototyping. Our approach is specifically tailored for domains in which effective prototypes and sub-groups of patients are assumed to exist, but groupings relevant to the training objective are not …

The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy

Publications and Research

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M^pro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of M^pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M^pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for M^pro, including …

Late Pleistocene And Early Holocene Sea-Level History And Glacial Retreat Interpreted From Shell-Bearing Marine Deposits Of Southeastern Alaska, Usa, James F. Baichtal, Alia J. Lesnek, Risa J. Carlson, Nicholas S. Schmuck, Jane L. Smith, Dennis J. Landwehr, Jason P. Briner

Publications and Research

We leverage a data set of >720 shell-bearing marine deposits throughout southeastern Alaska (USA) to develop updated relative sea-level curves that span the past ~14,000 yr. This data set includes site location, elevation, description when avail-able, and 436 14C ages, 45 of which are published here for the first time. Our sea-level curves suggest a peripheral forebulge developed west of the retreating Cordilleran Ice Sheet (CIS) margin between ca. 17,000 and 10,800 calibrated yr B.P. By 14,870 ± 630 to 12,820 ± 340 cal. yr B.P., CIS mar-gins had retreated from all of southeastern Alaska’s fjords, channels, and passages. At …

Teaching Artificial Intelligence In Technology And Engineering Education, Euisuk Sung

Publications and Research

No abstract provided.

Identity Selection And The Social Construction Of Birthdays, Brett W. Pelham, Tracy Dehart, Mitsuru Shimizu, Curtis D. Hardin, H. Anna Han, William Von Hippel

Publications and Research

We argue that rather than being a wholly random event, birthdays are sometimes selected by parents. We further argue that such effects have changed over time and are the result of important psychological processes. Long ago, U.S. American parents greatly overclaimed holidays as their children’s birthdays. These effects were larger for more important holidays, and they grew smaller as births moved to hospitals and became officially documented. These effects were exaggerated for ethnic groups that deeply valued specific holidays. Parents also overclaimed well-liked calendar days and avoided disliked calendar days as their children’s birthdays. However, after birthday selection effects virtually …

Tailoring Plasmon Excitations In Alpha − T 3 Armchair Nanoribbons, Andrii Iurov, Liubov Zhemchuzhna, Godfrey Gumbs, Danhong Huang, Paula Fekete, Farhana Anwar, Dipendra Dahal, Nicholas Weekes

Publications and Research

We have calculated and investigated the electronic states, dynamical polarization function and the plasmon excitations for α − T ₃ nanoribbons with armchair-edge termination. The obtained plasmon dispersions are found to depend significantly on the number of atomic rows across the ribbon and the energy gap which is also determined by the nanoribbon geometry. The bandgap appears to have the strongest effect on both the plasmon dispersions and their Landau damping. We have determined the conditions when relative hopping parameter α of an α − T ₃ lattice has a strong effect on the plasmons which makes our material distinguished …

Crossing The Great Divide: Bridging The Researcher–Practitioner Gap To Maximize The Utility Of Remote Sensing For Invasive Species Monitoring And Management, Kelsey Parker, Arthur Elmes, Peter Boucher, Richard A. Hallett, John E. Thompson, Zachary Simek, Justin Bowers, Andrew B. Reinmann

Advanced Science Research Center

Invasive species are increasingly present in our ecosystems and pose a threat to the health of forest ecosystems. Practitioners are tasked with locating these invasive species and finding ways to mitigate their spread and impacts, often through costly field surveys. Meanwhile, researchers are developing remote sensing products to detect the changes in vegetation health and structure that are caused by invasive species, which could aid in early detection and monitoring efforts. Although both groups are working towards similar goals and field data are essential for validating RS products, these groups often work independently. In this paper, we, a group of …

Graduate Student Employee Unionization In The Second Gilded Age, William A. Herbert, Joseph Van Der Naald

Publications and Research

In debates on the future of work, a common theme has been how work became
less secure through the denial of employee status. Though much of the attention
has focused on other industries, precarity has also affected those working in
higher education, including graduate student employees, contributing to what is
now called the “gig academy.” While universities have reassigned teaching and
research to graduate assistants, they have also refused to recognize them as
employees. Nevertheless, unionization has grown considerably since 2012, most
significantly at private institutions. Utilizing a unique dataset, this chapter
demonstrates that between 2012 and 2019, graduate student …

Tectonic And Geotechnical Review Of Bengal Basin For Seismic Risk Assessment In Bangladesh, Mir Fazlul Karim, Jnana Ranjan Kayal, Daya Shanker, Nazrul I. Khandaker, Arif M. Sikder, M Zillur Rahman, Muhammad Qumrul Hassan

Publications and Research

Four major geotectonic provinces of the basin are recognized: 1) the continental slope to the west of the Hinge Zone, 2) the stable shelf, 3) the deep central trough (Sylhet-Hatiya) and 4) the Chittagong-Tripura fold belt to the east. The ~300 km long Dauki Fault demarcates the elevated Shillong Plateau, part of the Indian Shield to the north and the deep basin to the south. The basin experienced three strong to major intraplate earthquakes: a) 1885 Bengal earthquake (rev. Mw 6.8) close to the Hinge Zone, b) 1918 Srimangal earthquake (rev. Mw 7.1) on the Sylhet (trough) fault and c) …

Addressing The Learning Loss During The Covid-19 Pandemic Through The Adaptation Of Virtual Platforms, Nazrul I. Khandaker, Anika Nawar Mayeesha, Violeta Escandon Correa, Toralv Munro, Andrew Singh, Matthew Khargie, Ality Aghedo, Jasmin Budhan, Krishna Mahabir, Belal A. Sayeed

Publications and Research

The York College-hosted NASA MAA (MUREP AEROSPACE ACADEMY) has always played a pivotal role in minimizing the learning loss during the summer months, which was heightened during the pandemic. Support from AT&T, Con Edison and NASA enabled the MAA program at York College to offer a virtual STEM education with an earth science concentration to 1000 plus underserved K1-12 students from the community last summer, including 160 high school students. Two factors made this endeavor fruitful: allowing additional time to engage in STEM lessons and increasing self-motivation to successfully accomplish assigned tasks. Students built partnerships and resolved technical issues with …

Determination Of Sustainable Zones For Groundwater Abstraction From The Multi-Layered Aquifer System In The Bengal Basin, Bangladesh, Anwar Zahid, Muhammad Qumrul Hassan, Nazrul I. Khandaker

Publications and Research

The use of deep groundwater (±300 m deep) is becoming an important issue in the Bengal Basin, due to both water quality problems and an acute shortage of available water in upper aquifers. In southeastern Bangladesh, multi-layered aquifer conditions exist with arsenic contamination at shallow depths, and high iron and brackish groundwater occurring mainly in the deeper layers. Many previous studies have offered explanations for the high concentrations of dissolved arsenic in groundwater - most of which proposed that the arsenic is derived from geo-genic sources and its release in groundwater is through natural processes, not the result of anthropogenic …

Leveraging The Popularity Of Virtual Conferencing Due To The Covid-19 Pandemic To Create New Opportunities For Stem Education, Andrew Singh, Nazrul I. Khandaker, Violeta Escandon Correa, Omadevi Singh, Ariel Skobelsky, Farhan Tanvir, Brian Sukhnandan, Matthew Khargie, Elton Selby, Masud Ahmed

Publications and Research

Due to the COVID-19 pandemic, virtual learning has become a necessity for K9-16 education. Virtual classwork has been administered through platforms such as Google Classroom, Clever, and iReady. During the summer of 2021, the City University of New York (C.U.N.Y) York College campus hosted its NASA MAA MUREP (Minority University Research and Education Project Aerospace Academy) program virtually using a combination of Zoom, Google Docs, and even Canva, which some students requested as a more intuitive alternative to Microsoft PowerPoint. Students were mentored to use the scientific method to explore their interests in the STEM field, with a geoscience or …

The Importance Of Monitoring To Assess The Impact Of Climate Change On Groundwater Resources In Bangladesh, Muhammad Qumrul Hassan, Anwar Zahid, Nazrul I. Khandaker

Publications and Research

Groundwater is the major source of fresh water across much of the world, but there has been very little study on the impacts of climate change on this precious and finite resource. Rising levels of greenhouse gases are likely to increase the global average surface temperature over the next 100 years, raise sea levels and reduce soil moisture. The amount of water stored in the soil is fundamentally important to agriculture and influences the rate of actual evaporation, groundwater recharge and runoff. Rising sea levels would cause the tidal saltwater wedge to intrude further upstream in rivers, with resulting changes …

Multi-Faceted Geoscience Research Using Open Access Resources: The Successful Participation Of K9-16 Students, Nazrul I. Khandaker, Noshin Sharmili, Omadevi Singh, Gurwinder Sahota, Sol De Leon, Matthew Khargie, Ali Zarine, Krishna Mahabir, Adacia Teemal, Mildred M. Selby

Publications and Research

Students interested in geosciences, for the most part, missed out their traditional field- based research activities due to strict social distancing, travel restrictions and/or lacking financial support. An absence of physical laboratory opportunities forced students to choose topics deemed doable through online research. Available data from online sources on extreme weather related case studies, flooding, droughts, groundwater depletion in urban and suburban areas, coastal erosion rate, sealevel rise, landslides, earthquakes, volcanic eruptions, and atmospheric pollution became quite handy and lucrative. Readily available pertinent data sources enabled K9-16 students to conduct summer research at “stay home” situations. Selective peer mentoring was …

Assessment Of The Impacts Of Urbanization On Land-Use And Land-Cover Changes Using Remote Sensing And Python At Gazipur District, Bangladesh, Atika Rahman Akji, Nowshin Ahsan Priyanka, Anwar Zahid, Muhammad Qumrul Hassan, Jowaher Raza, Nazrul I. Khandaker

Publications and Research

Urbanization has been the central demographic trend, not only in the Asia-Pacific region, but also for the entire world. Local geo-mapping is the vital tool for analyses of land-use and land-cover. This study attempts to classify land-use in unsupervised settings and create land-cover map by using open-source Landsat data integrated with GIS technologies and other ancillary resources. This work concentrates on Gazipur Sadar (an upazila or sub-district of the Gazipur District in central Bangladesh, part of the Dhaka Division) and Kaliakair, which are rapidly growing unplanned urban and industrial zones. The usage of python coding greatly assisted accomplishing the post-classification …

Statistical Analysis Of Groundwater Level Fluctuation Of The Urban And Peri-Urban Area Of Gazipur District, Bangladesh, Nowshin Ahsan Priyanka, Atika Rahman Akji, Anwar Zahid, Muhammad Qumrul Hassan, Jowaher Raza, Nazrul I. Khandaker

Publications and Research

Groundwater is the primary source for drinking, municipal, irrigation, and industrial water supply in Bangladesh. Due to unplanned urbanization and rapidly growing industries, the degradation situation has become perilous over time. Dhaka and its peri-urban regions are having drastic changes in groundwater (GW) levels. This work reviewed GW level fluctuation in the peri-urban area, which is now severely experiencing the detrimental impact of rapid urbanization and industrialization. Detail statistical investigation and Landsat image interpretation of the study area was conducted. Analysis and prediction of water level trends were conducted using variations of Mann Kendell tests. Gazipur Sadar (an upazila or …

Wave Function Identity: A New Symmetry For 2-Electron Systems In An Electromagnetic Field, Marlina Slamet, Viraht Sahni

Publications and Research

Stationary-state Schrödinger-Pauli theory is a description of electrons with a spin moment in an external electromagnetic field. For 2-electron systems as described by the Schrödinger-Pauli theory Hamiltonian with a symmetrical binding potential, we report a new symmetry operation of the electronic coordinates. The symmetry operation is such that it leads to the equality of the transformed wave function to the wave function. This equality is referred to as the Wave Function Identity. The symmetry operation is a two-step process: an interchange of the spatial coordinates of the electrons whilst keeping their spin moments unchanged, followed by an inversion. The Identity …

Development Of Predictive Models For Water Budget Simulations Of Closed-Basin Lakes: Case Studies Of Lakes Azuei And Enriquillo On The Island Of Hispaniola, Mahrokh Moknatian, Michael Piasecki

Publications and Research

The historical water level fluctuations of the two neighboring Caribbean lakes of Azuei (LA) and Enriquillo (LE) on Hispaniola have shown random periods of synchronous and asynchronous behaviors, with both lakes exhibiting independent dynamics despite being exposed to the same climatic forces and being directly next to each other. This paper examines their systems' main drivers and constraints, which are used to develop numerical models for these two lakes. The water balance approach was employed to conceptually model the lakes on an interannual scale and examine the assumptions of surface and subsurface processes. These assumptions were made based on field …

Teaching And Learning Mathematics In Secondary Schools, Despina Stylianou

Open Educational Resources

No abstract provided.

(2021 Revision) Chapter 4: Essential Aspects Of Physical Design And Implementation Of Relational Databases, Tatiana Malyuta, Ashwin Satyanarayana

Open Educational Resources

No abstract provided.

Earth System Science, Karin A. Block

Open Educational Resources

Syllabus for 4-credit introductory earth system science course covering three units: 1. The Solid Earth; 2. The Fluid Envelope; 3. Climate and Natural Resources. Format is lecture plus 3 hr lab.

Globe Mosquito Habitat Mapper Citizen Science Data 2017–2020, Russanne Low, Rebecca Boger, Peder Nelson, Matteo Kimura

Publications and Research

The GLOBE Program's GLOBE Observer application is a free citizen science mobile data collection and visualization tool compatible with iOS and Android operating systems. Citizen scientists armed with the app can report the mosquito larval habitats they identify using the GLOBE Mosquito Habitat Mapper tool. This data can complement the climate, weather, and land cover data obtained from satellite measurements by scientists who develop risk models for mosquito-borne diseases. Public participation in mosquito surveillance research provides the opportunity to obtain the volume, velocity and variety of data needed to fight the threat of vector-borne diseases, especially in under-resourced communities with …

Introduction To Discrete Mathematics: An Oer For Ma-471, Mathieu Sassolas

Open Educational Resources

The first objective of this book is to define and discuss the meaning of truth in mathematics. We explore logics, both propositional and first-order , and the construction of proofs, both formally and human-targeted. Using the proof tools, this book then explores some very fundamental definitions of mathematics through set theory. This theory is then put in practice in several applications. The particular (but quite widespread) case of equivalence and order relations is studied with detail. Then we introduces sequences and proofs by induction, followed by number theory. Finally, a small introduction to combinatorics is …

Syllabus, Loren Cohen

Open Educational Resources

No abstract provided.