Digital Commons Network^™

Evaluation Of Log P, Pka, And Log D Predictions From The Sampl7 Blind Challenge, Teresa Danielle Bergazin, Nicolas Tielker, Yingying Zhang, Junjun Mao, M. R. Gunner, Karol Francisco, Carlo Ballatore, Stefan M. Kast, David L. Mobley

Publications and Research

The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges focuses the computational modeling community on areas in need of improvement for rational drug design. The SAMPL7 physical property challenge dealt with prediction of octanol-water partition coefficients and pK_a for 22 compounds. The dataset was composed of a series of N-acylsulfonamides and related bioisosteres. 17 research groups participated in the log P challenge, submitting 33 blind submissions total. For the pK_a challenge, 7 different groups participated, submitting 9 blind submissions in total. Overall, the accuracy of octanol-water log P predictions in the SAMPL7 challenge was …

The Effect Of Fluid Flow Shear Stress And Substrate Stiffness On Yes-Associated Protein (Yap) Activity And Osteogenesis In Murine Osteosarcoma Cells, Thomas R. Coughlin, Ali Sana, Kevin Voss, Abhilash Gadi, Upal Basu-Roy, Caroline M. Curtin, Alka Mansukhani, Oran D. Kennedy

Publications and Research

Osteosarcoma (OS) is an aggressive bone cancer originating in the mesenchymal lineage. Prognosis for metastatic disease is poor, with a mortality rate of approximately 40%; OS is an aggressive disease for which new treatments are needed. All bone cells are sensitive to their mechanical/ physical surroundings and changes in these surroundings can affect their behavior. However, it is not well understood how OS cells specifically respond to fluid movement, or substrate stiffness—two stimuli of relevance in the tumor microenvironment. We used cells from spontaneous OS tumors in a mouse engineered to have a bone-specific knockout of pRb-1 and p53 in …

Preventing Transmission Of Covid 19 In Hvac Duct Systems: Implementations Of Hvac System Design Upgrade, Jacob S. Lopez, Adama Barro

Publications and Research

The recent pandemic outbreak has triggered a global alarm to increase efforts on finding the best methods to mitigate contagious viral pathogens. This project is a continuation of our mission to study engineering guidelines needed to implement upgrades to HVAC Systems in order to deter airborne pathogens such as the covid-19 virus. In our previous projects we researched how covid-19 can possibly flow through the ambient air inside of restaurants, office spaces, and locomotive train cabins. As we continued our research, we were able to find some solutions that will be best used to deactivate and prevent the virus from …

Sites Of Circadian Clock Neuron Plasticity Mediate Sensory Integration And Entrainment, Maria P. Fernand, Hannah L. Pettibone, Joseph T. Bogart, Casey J. Roell, Charles E. Davey, Ausra Pranevicius, Khang V. Huynh, Sara M. Lennox, Boyan Kostadinov, Orie T. Shafer

Publications and Research

Networks of circadian timekeeping in the brain display marked daily changes in neuronal morphology. In Drosophila melanogaster, the striking daily structural remodeling of the dorsal medial termini of the small ventral lateral neurons has long been hypothesized to mediate endogenous circadian timekeeping. To test this model, we have specifically abrogated these sites of daily neuronal remodeling through the reprogramming of neural development and assessed the effects on circadian timekeeping and clock outputs. Remarkably, the loss of these sites has no measurable effects on endogenous circadian timekeeping or on any of the major output functions of the small ventral lateral neurons. …

Area Characteristics And Consumer Nutrition Environments In Restaurants: An Examination Of Hispanic Caribbean Restaurants In New York City, Melissa Fuster, Hanish Kodali, Krishnendu Ray, Brian Elbel, Margaret A. Handley, Terry T. Huang, Glen Johnson

Publications and Research

Hispanics in the USA, particularly those of Caribbean descent, experience high levels of diet-related diseases and dietary risk factors. Restaurants are an increasingly important yet understudied source of food and may present opportunities to positively influence urban food environments. We sought to explore food environments further, by examining the association between neighborhood characteristics and restaurant consumer nutrition environments within New York City’s Hispanic Caribbean (HC) restaurant environments. We applied an adapted version of the Nutrition Environment Measurements Survey for Restaurants (NEMS-R) to evaluate a random sample of HC restaurants (n=89). NEMS-HCR scores (continuous and categorized as low, medium, and high …

The Wizard Of Roz, Marleen S. Barr

Publications and Research

In this humorous short story by Marleen S. Barr an emissary from the planet Roz and a dragon who lives in an invisible tree inside Trump Tower save America from the Big Lie.

All-Optical Nonreciprocity Due To Valley Polarization Pumping In Transition Metal Dichalcogenides, Sriram Guddala, Yuma Kawaguchi, Filipp Komissarenko, Svetlana Kiriushechkina, Anton Vakulenko, Kai Chen, Andrea Alù, Vinod M. Menon, Alexander B. Khanikaev

Publications and Research

Nonreciprocity and nonreciprocal optical devices play a vital role in modern photonic technologies by enforcing one-way propagation of light. Here, we demonstrate an all-optical approach to nonreciprocity based on valley-selective response in transition metal dichalcogenides (TMDs). This approach overcomes the limitations of magnetic materials and it does not require an external magnetic field. We provide experimental evidence of photoinduced nonreciprocity in a monolayer WS2 pumped by circularly polarized (CP) light. Nonreciprocity stems from valley-selective exciton population, giving rise to nonlinear circular dichroism controlled by CP pump fields. Our experimental results reveal a significant effect even at room temperature, despite considerable …

Quantifying The Speed Of Chromatophore Activity At The Single-Organ Level In Response To A Visual Startle Stimulus In Living, Intact Squid, Stavros P. Hadjisolomou, Rita W. El-Haddad, Kamil Kloskowski, Alla Chavarga, Israel Abramov

Publications and Research

The speed of adaptive body patterning in coleoid cephalopods is unmatched in the natural world. While the literature frequently reports their remarkable ability to change coloration significantly faster than other species, there is limited research on the temporal dynamics of rapid chromatophore coordination underlying body patterning in living, intact animals. In this exploratory pilot study, we aimed to measure chromatophore activity in response to a light flash stimulus in seven squid, Doryteuthis pealeii. We video-recorded the head/arms, mantle, and fin when squid were presented with a light flash startle stimulus. Individual chromatophores were detected and tracked over time using image …

Remission Of Type 2 Diabetes With Very Low-Calorie Diets —A Narrative Review, Susan Juray, Kathleen V. Axen, Steven Trasino

Publications and Research

Very low-calorie diets (VLCD) are hypocaloric dietary regimens of approximately 400–800 kcal/day that result in 20–30% reductions in body weight, sometimes in just 12–16 weeks. A body of evidence demonstrates that adherence to VLCD in adults with type 2 diabetes (T2D) can result in marked improvements to glycemic control and even full T2D remission, challenging the convention that T2D is a lifelong disease. Although these data are promising, the majority of VLCD studies have focused on weight loss and not T2D remission as a primary endpoint. Moreover, there is a wide range of VLCD protocols and definitions of T2D remission …

Atypical Presentation Of Esophageal Squamous Cell Carcinoma Masquerading As Diffuse Severe Esophagitis, Hafsa Abbas, Haider Ghazanfar, Ali Naqqi Ul Hussain, Ahmed Baiomi, Ariyo Ihimoyan

Publications and Research

Esophagitis is described as an inflammation of the esophagus and can result from multiple etiologies. Esophageal squamous cell carcinoma (ESCC), presenting as diffuse esophagitis in the absence of a mass or lesion, is rare. We present a case of a 61-year-old man who presented to the gastroenterology clinic for dysphagia and heartburn of 3 months duration. The patient had lost about 15 pounds unintentionally over 6 months. The patient underwent esophagogastroduodenoscopy, which revealed significant diffuse Grade 4 esophagitis without any overt bleeding. Random biopsies were taken with cold forceps from proximal, middle, and distal esophageal segments because of the striking …

Annotated Genome Sequence Of The High-Biomass-Producing Yellow-Green Alga Tribonema Minus, Kristina M. Mahan, Jüergen E.W. Polle, Zaid Mckie-Krisberg, Anna Lipzen, Alan Kuo, Igor V. Grigoriev, Todd W. Lane, Aubrey K. Davis

Publications and Research

Here, we report the annotated genome sequence for a heterokont alga from the class Xanthophyceae. This high-biomass-producing strain, Tribonema minus UTEX B 3156, was isolated from a wastewater treatment plant in California. It is stable in outdoor raceway ponds and is a promising industrial feedstock for biofuels and bioproducts.

Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner

Publications and Research

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome …

Covid-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning, Yang Liu, You Wu, Xiaoke Shen, Lei Xie

Publications and Research

The life-threatening disease COVID-19 has inspired significant efforts to discover novel therapeutic agents through repurposing of existing drugs. Although multi-targeted (polypharmacological) therapies are recognized as the most efficient approach to system diseases such as COVID-19, computational multi-targeted compound screening has been limited by the scarcity of high-quality experimental data and difficulties in extracting information from molecules. This study introduces MolGNN , a new deep learning model for molecular property prediction. MolGNN applies a graph neural network to computational learning of chemical molecule embedding. Comparing to state-of-the-art approaches heavily relying on labeled experimental data, our method achieves equivalent or superior prediction …

Fostering Information Literacy: A Call For Collaboration Between Academic Librarians And Msw Instructors., Sarah C. Johnson, Margaret Bausman, Sarah Ward

Publications and Research

Genuine collaboration between academic librarians and social work faculty in which information literacy is embedded in social work education is lacking. Drawing from the results of the authors’ 2016 quantitative study surveying academic social work librarians across the United States, this qualitative follow-up uses data from 27 semi-structured interviews concerning the prevalence and nature of information literacy instruction (ILI) in social work education, how ILI is introduced and sustained in social work curricula, and the alignment between ILI efforts with institutional goals, guidelines from accreditation authorities, and professional social work practice standards. The literature review engages the reader in a …

Measuring Procedural Justice Policy Adherence During Use Of Force Events: The Body-Worn Camera As A Performance Monitoring Tool, Victoria A. Sytsma, Eric L. Piza, Vijay F. Chillar, Leigh S. Grossman

Publications and Research

This study capitalizes on a successful researcher–practitioner partnership to conduct a systematic social observation (SSO) of police body-worn camera (BWC) footage in Newark, NJ. To demonstrate the utility of BWCs as performance monitoring tools, we measure officer adherence to procedural justice standards throughout use of force events as mandated in the Newark Police Division’s updated policies pursuant to an ongoing federal consent decree. Overall, a slim majority of use of force events are procedurally just. However, results indicate several instances of policy noncompliance. Results are discussed, and policy recommendations related to procedural justice policy violations and BWCs for performance monitoring …

Admissions Of Covid-Positive Patients To Us Nursing Homes With Personal Protective Equipment Or Staffing Shortages, Diane M. Gibson, Jessica Greene

Publications and Research

Background: US nursing homes are required to follow Centers for Disease Control guidance for COVID-19 transmission-based precautions (TBP) when admitting COVID-positive patients.

Objective: To assess how frequently nursing homes had shortages of personal protective equipment (PPE) or staffing in weeks when they admitted COVID-positive patients, which likely made it more difficult to follow TBP, and to compare facility characteristics by admissions practices.

Design and Setting: Facility-level data from the Nursing Home COVID-19 Public File for the period between June 7, 2020 and March 7, 2021 was combined with additional data. The percentages of nursing homes that admitted COVID-positive patients and …

First Report Of Mummenhoffia Alliacea (Brassicaceae) For New York, Daniel Atha, Eve Levine, John F. Gaskin, César Castillo

Publications and Research

Mummenhoffia alliacea is naturalized in New York. The first documented occurrences are reported from Dutchess, Kings, New York (Manhattan), Onondaga, Queens, and Suffolk counties. Verification is provided by herbarium specimens at NY and photographs uploaded to iNaturalist and cited at the Global Biodiversity Information Facility.

Adapting To The Pandemic: Experiences Of Latin American Restaurants During Covid-19 And Potential Implications For Community Health And Food Environments, Elise Harrison, Michelle Rodriguez, Diana Veliz, Rosa Abreu, Melissa Fuster

Publications and Research

Objectives

Assess how Latin American restaurants (LAR) have been adapting in response to COVID-19, and the potential implications of those changes for community food environments.

Book Review, Abalone: The Remarkable History And Uncertain Future Of California’S Iconic Shellfish, Claire Stewart

Publications and Research

No abstract provided.

Facilitating Healthy Eating In Latin American Restaurants: Examining Acceptability And Barriers Among Restaurant Owners And Staff, Melissa Fuster, Rosa Abreu, Terry T-K Huang, Michelle Rodriguez, Elise Harrison, Brian Elbel, Krishnendu Ray, Margaret Handley

Publications and Research

Objectives: Examine the acceptability and potential barriers for the implementation of healthy eating promoting (HEP) strategies in independently-owned Latin American restaurants (LAR), including the influence of the COVID-19 pandemic.

Defining The Basis Of Cyanine Phototruncation Enables A New Approach To Single-Molecule Localization Microscopy, Siddharth S. Matikonda, Dominic A. Helmerich, Mara Meub, Gerti Beliu, Philip Kollmannsberger, Alexander Greer, Markus Sauer, Martin J. Schnermann

Publications and Research

The light-promoted conversion of extensively used cyanine dyes to blue-shifted emissive products has been observed in various contexts. However, both the underlying mechanism and the species involved in this photoconversion reaction have remained elusive. Here we report that irradiation of heptamethine cyanines provides pentamethine cyanines, which, in turn, are photoconverted to trimethine cyanines. We detail an examination of the mechanism and substrate scope of this remarkable twocarbon phototruncation reaction. Supported by computational analysis, we propose that this reaction involves a singlet oxygeninitiated multistep sequence involving a key hydroperoxycyclobutanol intermediate. Building on this mechanistic framework, we identify conditions to improve the …

Draft Genome Sequences Of 13 Vibrio Cholerae Strains From The Rio Grande Delta, Jeffrey W. Turner, Jorge Duran-Gonzalez, David A. Laughlin, Daniel Unterweger, David Silva, Boris Ermolinsky, Stefan Pukatzki, Daniele Provenzano

Publications and Research

Vibrio cholerae is the etiologic agent of cholera, an acute and often fatal diarrheal disease that affects millions globally. We report the draft genome sequences of 13 non-O1/O139 V. cholerae strains isolated from the Rio Grande Delta in Texas. These genomes will aid future analyses of environmental serovars.

Detection Methods And Clinical Applications Of Circulating Tumor Cells In Breast Cancer, Hongyi Zhang, Xiaoyan Lin, Yuan Huang, Minghong Wang, Chunmei Cen, Shasha Tang, Marcia R. Dique, Lu Cai, Manuel A. Luis, Jillian Smollar, Yuan Wan, Fengfeng Cai

Publications and Research

Circulating Tumor Cells (CTCs) are cancer cells that split away from the primary tumor and appear in the circulatory system as singular units or clusters, which was first reported by Dr. Thomas Ashworth in 1869. CTCs migrate and implantation occurs at a new site, in a process commonly known as tumor metastasis. In the case of breast cancer, the tumor cells often migrate into locations such as the lungs, brain, and bones, even during the early stages, and this is a notable characteristic of breast cancer. Survival rates have increased significantly over the past few decades because of progress made …

Instructional Design With The Ice Approach In Academic Libraries: A Framework That Integrates Assessing, Learning, And Teaching, Junli Diao

Publications and Research

One-shot instruction in academic libraries is a librarian-controlled bibliographic instruction that responds to the point of information need for subject-related courses. The assessment of teaching effectiveness tends to take a summative approach, which provides an answer to what students learned but does not address how they learned. This column theoretically explores the framework of Ideas-Connections-Extensions (ICE) in library instruction and the classroom setting, which demonstrates learning outcomes and explores the learning journey, and integrates assessment, learning, and teaching through collaborative efforts by academic librarians and classroom faculty.

Assessment Of Judgment Ability In A Brazilian Sample Of Patients With Mild Cognitive Impairment And Dementia, Patrícia Helena Figueirêdo Do Vale-Britto, Laura Rabin, Livia Spindola, Ricardo Nitrini, Sonia Maria Dozzi Brucki

Publications and Research

Judgment is the ability to make sound decisions after consideration of relevant information, possible solutions, likely outcomes, and contextual factors. Loss of judgment is common in patients with mild cognitive impairment (MCI) and dementia. The Test of Practical Judgment (TOP-J) evaluates practical judgment in adults and the elderly, with 15- and 9-item versions that require individuals to listen to scenarios about everyday problems and report their solutions. Objective: Adaptation of TOP-J for a Brazilian sample, preparation of a reduced version and verification of the accuracy of both. Methods: Eighty-five older adults, including 26 with MCI, 20 with Alzheimer’s disease (AD), …

Digital Exhibition: Romaniote Memories, A Jewish Journey From Ioannina, Greece To Manhattan, Annie E. Tummino, Nicholas Alexiou

Publications and Research

This article discusses creation of the digital exhibition, Romaniote Memories, a Jewish Journey from Ioannina, Greece to Manhattan: Photographs by Vincent Giordano at Queens College, City University of New York.

Disruption, Transition, Adaptation: Archivists Working Under Covid-19, Annie E. Tummino, Tomasz Gubernat, Jeanie Pai, Victoria Fernandez, Kuba Pieczarski, Patricia Reguyal, Caitlin Colban-Waldron

Publications and Research

In this lightning round session, panelists discuss how a small but spirited archive is adapting to work during the COVID-19 pandemic. Since Queens College Special Collections and Archives is largely staffed by current and recent graduates of the college's graduate program in Library and Information Studies, this is a special opportunity to hear from a diverse group of emerging professionals during a challenging and rapidly changing time in the field.

Depression, Depression Literacy, And Sociodemographic Characteristics Of Korean Americans: A Preliminary Investigation, Kunsook Bernstein, Young-Me Lee, Philmon N. Gona, Shinhi Han, Soonsik Kim, Sun S. Kim

Publications and Research

Despite the rapid growth in the number of Korean Americans (KAs) and the alarmingly high prevalence of depression in this population, relatively little is known about the impact of depression literacy on KAs’ depression. This study investigated the prevalence of depressive symptoms among a community-based sample of KA adults; the associations among socio-demographic characteristics, depression literacy, and depressive symptoms; and predictors related to depressive symptoms. A sample of 600 KAs completed depression and depression literacy scales, as well as socio-demographic questionnaires. Data analyses were conducted to assess the association between depressive symptoms, depression literacy, and the covariates. Forty-five percent of …

Correlates Of Exam Performance In An Introductory Statistics Course: Basic Math Skills Along With Self- Reported Psychological/Behavioral And Demographic Variables, Laura A. Rabin, Anjali Krishnan, Rose Bergdoll, Joshua Fogel

Publications and Research

This study investigated whether basic mathematics skills are associated with undergraduate psychology statistics course performance while simultaneously considering self-reported psychological/behavioral and demographic variables. Participants (n = 460) completed a Math Assessment for College Students (MACS), which included questions ranging from calculating percentages to graphical interpretation. The researchers used a discriminant correspondence analysis to reveal differences in course performance evaluated as the average of three exam grades. For the variation in the average exam scores accounted for by our model, the MACS scores provided the largest contribution. Other variables associated with better exam grades included white ethnicity, non-transfer status, lower year …

Getting To Work: Information Literacy Instruction, Career Courses, And Digitally Proficient Students, Alexandra Hamlett

Publications and Research

This article discusses how following graduation, students often enter the job market unprepared to find, evaluate, and use information in the digital environment effectively. Essentially, there is a disparity between the skills students attain in college coursework, including information literacy (IL) skills, and those required in the workplace, which impacts graduates’ success as new members of the labour market. The article highlights how collaboration between a librarian and an instructor of a career centered course influenced instructional design for IL instruction in their courses. Librarians and instructors will benefit from practical examples from Guttman Community College’s innovative IL Program and …