Digital Commons Network^™

Potential Solar Replacement Of Hydroelectricity To Reopen Rivers: Maine As A Case Example, Shailesh Sharma, John Waldman

Publications and Research

Hydroelectricity provides 6% of U.S. electrical power needs, but hydro-dams also cause environmental harm, including the retardation or complete blockage of spawning runs of anadromous fishes. To facilitate fish movements, engineered-fishways have long been used but many have performed poorly. Dam-removal is the most effective way of restoring dwindling migratory fish populations by allowing unrestricted pathways to their spawning areas and for the downstream migrations of post-spawning adults and juveniles. However, removals of hydro-dams result in a loss of electricity production. For the replacement of energy foregone from hydro-dam removals, various alternative energy installations are now feasible. We present one-to-one …

Beyond Bostock: Implications For Lgbtq+ Theory And Practice., Sean Mccandless, Nicole M. Elias

Publications and Research

The recent U.S. Supreme Court ruling in Bostock v. Clayton County is a landmark piece of case law that offers fundamental rights to LGBT persons. This essay reflects on how this case arrived at the Supreme Court and its implications for theory and praxis. The overall conclusion is that cautious optimism is warranted.

Geoprivacy, Convenience, And The Pursuit Of Anonymity In Digital Cities, Jerome Dobson, William A. Herbert

Publications and Research

Cities demand spatial efficiencies that can be achieved only through sharing of information. Current technologies support collection, processing, and dissemination of unprecedented quantities of personal, public, and corporate information. Inherent in this milieu is an inevitable contest among societal efficiency, corporate profits, consumer convenience, personal privacy, and even freedom. The authors examine current trends in technology, data collection, legislation, and public acceptance. They find that without broad specific regulations limiting location data collection and use—including a universal protected right for individuals to pursue anonymity—governments, commercial enterprises, employers, and individuals increasingly will exploit tracking technologies at the expense of geoprivacy.

Exploring New Pltl Modalities, Forging New Alliances, Nadia Kennedy, Ariane Masuda

Publications and Research

This essay focuses on rethinking and reimagining elements of a PLTL program, and on the new modalities to meet challenges of online undergraduate mathematics courses and rising demands for flexible student support. It examines advantages and challenges as found in the Integrated PLTL and Virtual Peer-Led Mathematics Study Groups, including issues such as meeting protocols, and the selection and training of peer leaders. Finally, it discusses an alliance with the college’s mathematics education program, which allows the PLTL program to draw on senior prospective teachers to co-organize and facilitate virtual study groups supporting undergraduate mathematics courses.

The Relationships Between Spawning Horseshoe Crabs And Egg Densities: Recommendations For The Assessment Of Populations And Habitat Suitability, Mark L. Botton Phd, Christina P. Colon Phd, Matthew Sclafani Phd, Robert E. Loveland Phd, Susan Elbin Phd, Kaitlyn Parkins

Publications and Research

1. Horseshoe crab population sizes and trends have been previously studied using surveys of spawning adults and counts of eggs from surface (top 5 cm) and deep (20 cm) sediment samples. The correlations between surface and deep eggs were studied at two locations, Delaware Bay and Jamaica Bay, USA, and the correlations between egg densities and spawning counts were examined in Jamaica Bay. 2. There were significantly higher densities of eggs in deep sediments than in surface sediments. Only about 10% of the variability in surface egg density was explained by deep egg density. The numerical patterns between surface and …

Jlsc Board Editorial 2021, Anne Gilliland, Rebekah Kati, Jennifer Solomon, Dave S. Ghamandi, Jill Cirasella, David Lewis, Dede Dawson

Publications and Research

It hardly needs to be said that 2020 was a difficult year for the world. COVID-19 has infected over 120 million people and killed over 2 million as of March 2021 (Johns Hopkins). At the same time, police violence against people of color continues, even as communities engage in long-overdue reckoning initiatives. Across the globe, researchers, governments, and communities needed quick, open, up-to-date information on testing for, treating, and preventing COVID-19. Our increased dependence on technology during lockdowns provided some with safety and continuity, while others experienced the widening of the digital divide. There is no greater urgency than the …

Extracellular Vesicles Released By Human Retinal Pigment Epithelium Mediate Increased Polarised Secretion Of Drusen Proteins In Response To Amd Stressors, Miguel Flores-Bellver, Jason Mighty, Silvia Aparicio-Domingo, Kang V. Li, Cui Shi, Jing Zhou, Hannah Cobb, Patrick Mcgrath, German Michelis, Patricia Lenhart, Ganna Bilousova, Søren Heissel, Michael J. Rudy, Christina Coughlan, Andrew E. Goodspeed, S. Patricia Becerra, Stephen Redenti, M. Valeria Canto-Soler

Publications and Research

Age-related macular degeneration (AMD) is a leading cause of blindness worldwide. Drusen are key contributors to the etiology of AMD and the ability to modulate drusen biogenesis could lead to therapeutic strategies to slow or halt AMD progression. The mechanisms underlying drusen biogenesis, however, remain mostly unknown. Here we demonstrate that under homeostatic conditions extracellular vesicles (EVs) secreted by retinal pigment epithelium (RPE) cells are enriched in proteins associated with mechanisms involved in AMD pathophysiology, including oxidative stress, immune response, inflammation, complement system and drusen composition. Furthermore, we provide first evidence that drusen-associated proteins are released as cargo of extracellular …

Human Retinal Organoids Release Extracellular Vesicles That Regulate Gene Expression In Target Human Retinal Progenitor Cells, Jing Zhou, Miguel Flores‑Bellver, Jianbo Pan, Alberto Benito‑Martin, Cui Shi, Onyekwere Onwumere, Jason Mighty, Jiang Qian, Xiufeng Zhong, Tasmim Hogue, Baffour Amponsah‑Antwi, Linda Einbond, Rajendra Gharbaran, Hao Wu, Bo‑Juen Chen, Zhiliang Zheng, Tatyana Tchaikovskaya, Xusheng Zhang, Hector Peinado, Maria Valeria Canto‑Soler, Stephen Redenti

Publications and Research

The mechanisms underlying retinal development have not been completely elucidated. Extracellular vesicles (EVs) are novel essential mediators of cell‑to‑cell communication with emerging roles in developmental processes. Nevertheless, the identification of EVs in human retinal tissue, characterization of their cargo, and analysis of their potential role in retina development has not been accomplished. Three‑dimensional retinal tissue derived from human induced pluripotent stem cells (hiPSC) provide an ideal developmental system to achieve this goal. Here we report that hiPSC‑derived retinal organoids release exosomes and microvesicles with small noncoding RNA cargo. EV miRNA cargo‑predicted targetome correlates with Gene Ontology (GO) pathways involved in …

Tracking The Racial Validity Of Placement By Probability, Annie M. Del Principe, Lesley Broder, Lauren Levesque

Publications and Research

Any placement decision is a gamble on the validity of the mech- anism used. The better the placement mechanism matches the actual pro- ficiencies required for success in a future, real-life context, the more accu- rately it will place students into the best classes for them and the more valid it will prove to be. But what happens if the most obvious, commonsensical approaches to placement that would appear to have the strongest validity— writing tests for placement into writing classes—prove unreliable? Rather than accurately placing students into the “right” class for them, we now know that writing placement tests …

African Land Mammal Ages, John Van Couvering, Eric Delson

Publications and Research

We define 17 African land mammal ages, or AFLMAs, covering the Cenozoic record of the Afro-arabian continent, the planet’s second largest land mass. While fossiliferous deposits are absent on the eroded plateau of the continent’s interior, almost 800 fossil genera from over 350 locations have now been identified in coastal deposits, karst caves, and in the Neogene rift valleys. Given a well-developed geochronologic framework, together with continuing revision to the fossil record—both stimulated by the story of human evolution in Africa—and also to compensate for the variation in fossil ecosystems across such great distances, the AFLMAs are biochronological units defined …

Enzymatic Analysis Of Yeast Cell Wall-Resident Gapdh And Its Secretion, Michael J. Cohen, Brianne Philippe, Peter N. Lipke

Publications and Research

In yeast, many proteins are found in both the cytoplasmic and extracellu- lar compartments, and consequently it can be difficult to distinguish nonconventional secretion from cellular leakage. Therefore, we monitored the extracellular glyceralde- hyde-3-phosphate dehydrogenase (GAPDH) activity of intact cells as a specific marker for nonconventional secretion. Extracellular GAPDH activity was proportional to the number of cells assayed, increased with incubation time, and was dependent on added substrates. Preincubation of intact cells with 100mM dithiothreitol increased the reac- tion rate, consistent with increased access of the enzyme after reduction of cell wall di- sulfide cross-links. Such treatment did not increase …

Africans Who Arrive In The United States Before 20 Years Of Age Maintain Both Cardiometabolic Health And Cultural Identity: Insight From The Africans In America Study, Elyssa M. Shoup, Thomas Hormenu, Nana H. Osei-Tutu, M.C. Sage Ishimwe, Arielle C. Patterson, Christopher W. Dubose, Annemarie Wentzel, Margrethe F. Horlyck-Romanovsky, Anne E. Sumner

Publications and Research

The overall consensus is that foreign-born adults who come to America age < 20 y achieve economic success but develop adverse behaviors (smoking and drinking) that lead to worse cardiometabolic health than immigrants who arrive age ≥ 20 y. Whether age of immigration affects the health of African-born Blacks living in America is unknown. Our goals were to examine cultural identity, behavior, and socioeconomic factors and determine if differences exist in the cardiometabolic health of Africans who immigrated to America before and after age 20 y. Of the 482 enrollees (age: 38 ± 1 (mean ± SE), range: 20–65 y) in the Africans in America cohort, 23% (111/482) arrived age < 20 y, and 77% (371/482) arrived age ≥ 20 y. Independent of francophone status or African region of origin, Africans who immigrated age < 20 y had similar or better cardiometabolic health than Africans who immigrated age ≥ 20 y. The majority of Africans who immigrated age < 20 y identified as African, had African-born spouses, exercised, did not adopt adverse health behaviors, and actualized early life migration advantages, such as an American university education. Due to maintenance of cultural identity and actualization of opportunities in America, cardiometabolic health may be protected in Africans who immigrate before age 20. In short, immigrant health research must be cognizant of the diversity within the foreign-born community and age of immigration.

Outlier Concepts Auditing Methodology For A Large Family Of Biomedical Ontologies, Ling Zheng, Hua Min, Yan Chen, Vipina Keloth, James Geller, Yehoshua Perl, George Hripcsak

Publications and Research

Background: Summarization networks are compact summaries of ontologies. The “Big Picture” view offered by summarization networks enables to identify sets of concepts that are more likely to have errors than control concepts. For ontologies that have outgoing lateral relationships, we have developed the "partial-area taxonomy" summarization network. Prior research has identified one kind of outlier concepts, concepts of small partials-areas within partial-area taxonomies. Previously we have shown that the small partial-area technique works successfully for four ontologies (or their hierarchies).

Methods: To improve the Quality Assurance (QA) scalability, a family-based QA framework, where one QA technique is potentially applicable to …

Missing Lateral Relationships In Top‑Level Concepts Of An Ontology, Ling Zheng, Yan Chen, Hua Min, P. Lloyd Hildebrand, Hao Liu, Michael Halper, James Geller, Sherri De Coronado, Yehoshua Perl

Publications and Research

Background: Ontologies house various kinds of domain knowledge in formal structures, primarily in the form of concepts and the associative relationships between them. Ontologies have become integral components of many health information processing environments. Hence, quality assurance of the conceptual content of any ontology is critical. Relationships are foundational to the definition of concepts. Missing relationship errors (i.e., unintended omissions of important definitional relationships) can have a deleterious effect on the quality of an ontology. An abstraction network is a structure that overlays an ontology and provides an alternate, summarization view of its contents. One kind of abstraction network is …

Extending Import Detection Algorithms For Concept Import From Two To Three Biomedical Terminologies, Vipina K. Keloth, James Geller, Yan Chen, Julia Xu

Publications and Research

Background: While enrichment of terminologies can be achieved in different ways, filling gaps in the IS-A hierarchy backbone of a terminology appears especially promising. To avoid difficult manual inspection, we started a research program in 2014, investigating terminology densities, where the comparison of terminologies leads to the algorithmic discovery of potentially missing concepts in a target terminology. While candidate concepts have to be approved for import by an expert, the human effort is greatly reduced by algorithmic generation of candidates. In previous studies, a single source terminology was used with one target terminology.

Methods: In this paper, we are extending …

Feasibility Of Continuous Fever Monitoring Using Wearable Devices, Benjamin L. Smarr, Kirstin Aschbacher, Sarah M. Fisher, Anoushka Chowdhary, Stephan Dilchert, Karena Puldon, Adam Rao, Frederick M. Hecht, Ashley E. Mason

Publications and Research

Elevated core temperature constitutes an important biomarker for COVID-19 infection; however, no standards currently exist to monitor fever using wearable peripheral temperature sensors. Evidence that sensors could be used to develop fever monitoring capabilities would enable large-scale health-monitoring research and provide high-temporal resolution data on fever responses across heterogeneous populations. We launched the TemPredict study in March of 2020 to capture continuous physiological data, including peripheral temperature, from a commercially available wearable device during the novel coronavirus pandemic. We coupled these data with symptom reports and COVID-19 diagnosis data. Here we report findings from the first 50 subjects who reported …

Trypanosoma Cruzi Modulates Piwi-Interacting Rna Expression In Primary Human Cardiac Myocytes During The Early Phase Of Infection, Kayla J. Rayford, Ayorinde Cooley, Ashutosh Arun, Girish Rachakonda, Yulia Kleschenko, Fernando Villalta, Siddharth Pratap, Maria F. Lima, Pius N. Nde

Publications and Research

Trypanosoma cruzi dysregulates the gene expression profile of primary human cardiomyocytes (PHCM) during the early phase of infection through a mechanism which remains to be elucidated. The role that small non-coding RNAs (sncRNA) including PIWI-interacting RNA (piRNA) play in regulating gene expression during the early phase of infection is unknown. To understand how T. cruzi dysregulate gene expression in the heart, we challenged PHCM with T. cruzi trypomastigotes and analyzed sncRNA, especially piRNA, by RNA-sequencing. The parasite induced significant differential expression of host piRNAs, which can target and regulate the genes which are important during the early infection phase. An …

Pandemic Vibrio Cholerae Shuts Down Site-Specific Recombination To Retain An Interbacterial Defence Mechanism, Francis J. Santoriello, Lina Michel, Daniel Unterweger, Stefan Pukatzki

Publications and Research

Vibrio cholerae is an aquatic microbe that can be divided into three subtypes: harmless environmental strains, localised pathogenic strains, and pandemic strains causing global cholera outbreaks. Each type has a contact-dependent type VI secretion system (T6SS) that kills neighbouring competitors by translocating unique toxic effector proteins. Pandemic isolates possess identical effectors, indicating that T6SS effectors may affect pandemicity. Here, we show that one of the T6SS gene clusters (Aux3) exists in two states: a mobile, prophage-like element in a small subset of environmental strains, and a truncated Aux3 unique to and conserved in pandemic isolates. Environmental Aux3 can be readily …

Open Educational Resources: What Do Students Want?, Aneeza Hussain, Joyette K. Noel

Publications and Research

This project aims at identifying the needs and requests of students for Open Educational Resources (OERs) in order to develop rubrics for design, evaluation but also revisions of OERs. For this purpose literature searches on the matter were conducted to determine if information on students’ perspective on OER content and expectations existed. Simultaneously, feedback from fellow City Tech students with experience using OERs has been collected. Our results provide insight on how City Tech students perceive OERs, in comparison with traditional resources. This also pinpoints the key pedagogical features that OERs should offer in order to attract, engage and better …

Testimony To The Cuny Board Of Trustees In Opposition To The Resolution To Approve A Contract With Turnitin For Plagiarism Detection Software, December 14th, 2020 Meeting, Luke Waltzer, Lisa M. Rhody, Roxanne Shirazi

Publications and Research

This statement was drafted in response to the Board of Trustee's consideration of a resolution to approve CUNY's contract renewal with Turnitin in 2020. The authors circulated the petition on December 3, 2020, and submitted the final version -- signed by 1065 members of the CUNY community -- to the Board of Trustees on December 7, 2020 for consideration at their meeting on December 14th, 2020.

Data Analysis And Visualizations Of Drosophila Behavioral Phases, Xiaona Zhou

Publications and Research

We analyze drosophila behavioral data from the neuroscience labs of Professor Maria de la Paz Fernandez, Barnard College of Columbia University, and Professor Orie Shafer, the Neuroscience Initiative of the CUNY Advanced Science Research Center. The main goal of this project is to create algorithms for analyzing and visualizing the average activity of drosophila across a specified number of days and across all live flies and use this analysis to calibrate a smoothing filter to be applied to the raw fly activity so that the drosophila behavioral phases can be computed and visualized. We also investigate how to compute and …

Improve The Prototype Of Low-Cost Near-Infrared Diffuse Optical Imaging System, Chen Xu, Mohammed Z. Shakil

Publications and Research

Diffuse Optical Tomography (DOT) and Optical Spectroscopy using near-infrared (NIR) diffused light has demonstrated great potential for the initial diagnosis of tumors and in the assessment of tumor vasculature response to neoadjuvant chemotherapy. The aims of this project are 1) to test the different types of LEDs in the near-infrared range, and design the driving circuit, and test the modulation of LEDs at different frequencies; 2) to test the APDs as a detector, and build the receiver system and compare efficiency with pre-built systems. In this project, we are focusing on creating a low-cost infrared transmission system for tumor and …

Unconventional Constituents And Shared Molecular Architecture Of The Melanized Cell Wall Of C. Neoformans And Spore Wall Of S. Cerevisiae, Christine Chrissian, Coney Pei-Chin Lin, Emma Camacho, Arturo Casadevall, Aaron M. Neiman, Ruth E. Stark

Publications and Research

The fungal cell wall serves as the interface between the cell and the environment. Fungal cell walls are composed largely of polysaccharides, primarily glucans and chitin, though in many fungi stress-resistant cell types elaborate additional cell wall structures. Here, we use solid-state nuclear magnetic resonance spectroscopy to compare the architecture of cell wall fractions isolated from Saccharomyces cerevisiae spores and Cryptococcus neoformans melanized cells. The specialized cell walls of these two divergent fungi are highly similar in composition. Both use chitosan, the deacetylated derivative of chitin, as a scaffold on which a polyaromatic polymer, dityrosine and melanin, respectively, is assembled. …

Proteomic Analysis Of Platelet-Rich And Platelet-Poor Plasma, Olga Miroshnychenko, Robert J. Chalkley, Ryan D. Leib, Peter A. Everts, Jason L. Dragoo

Publications and Research

Background

Autologous blood products, such as platelet-rich plasma (PRP) are commercial products broadly used to accelerate healing of tissues after injuries. However, their content is not standardized and significantly varies in composition, which may lead to differences in clinical efficacy. Also, the underlying molecular mechanisms for therapeutic effects are not well understood.

Purpose

A proteomic study was performed to compare the composition of low leukocyte PRP, platelet poor plasma (PPP), and blood plasma. Pathway analysis of the proteomic data was performed to evaluate differences between plasma formulations at the molecular level. Low abundance regulatory proteins in plasma were identified and …

Open Data, Collaborative Working Platforms, And Interdisciplinary Collaboration: Building An Early Career Scientist Community Of Practice To Leverage Ocean Observatories Initiative Data To Address Critical Questions In Marine Science, Robert M. Levine, Kristen E. Fogaren, Johna E. Rudzin, Christopher J. Russoniello, Dax C. Soule, Justine M. Whitaker

Publications and Research

Ocean observing systems are well-recognized as platforms for long-term monitoring of near-shore and remote locations in the global ocean. High-quality observatory data is freely available and accessible to all members of the global oceanographic community—a democratization of data that is particularly useful for early career scientists (ECS), enabling ECS to conduct research independent of traditional funding models or access to laboratory and field equipment. The concurrent collection of distinct data types with relevance for oceanographic disciplines including physics, chemistry, biology, and geology yields a unique incubator for cutting-edge, timely, interdisciplinary research. These data are both an opportunity and an incentive …

Reproducibility And Sensitivity Of Thirty-Six Methods To Quantify The Sars-Cov-2 Genetic Signal In Raw Wastewater: Findings From An Interlaboratory Methods Evaluation In The U.S., Brian M. Pecson, Emily Darby, Charles N. Haas, Yamrot M. Amha, Mitchel Bartolo, Richard Danielson, Yeggie Dearborn, George Di Giovanni, Christobel Ferguson, Stephanie Fevig, Erica Gaddis, Donald Gray, George Lukasik, Bonnie Mull, Liana Olivas, Adam Olivieri, Yan Qu, Sars-Cov-2 Interlaboratory Consortium, John J. Dennehy

Publications and Research

In response to COVID-19, the international water community rapidly developed methods to quantify the SARS-CoV-2 genetic signal in untreated wastewater. Wastewater surveillance using such methods has the potential to complement clinical testing in assessing community health. This interlaboratory assessment evaluated the reproducibility and sensitivity of 36 standard operating procedures (SOPs), divided into eight method groups based on sample concentration approach and whether solids were removed. Two raw wastewater samples were collected in August 2020, amended with a matrix spike (betacoronavirus OC43), and distributed to 32 laboratories across the U.S. Replicate samples analyzed in accordance with the project's quality assurance plan …

Immunohistochemical Localization Of Prolactin Receptor (Prlr) To Hodgkin's And Reed-Sternberg Cells Of Hodgkin's Lymphoma, Rajendra Gharbaran, Onyekwere Onwumere, Naomi Codrington, Latchman Somenarian, Stephen Redenti

Publications and Research

Prolactin receptor (PRLR), a type-1 cytokine receptor, is overexpressed in a number of cancer types. It has attracted much attention for putative pro-oncogenic roles, which however, remains controversial in some malignancies. In this study, we reported the localization of PRLR to the Hodgkin's and Reed-Sternberg (HRS) cells of Hodgkin's lymphoma (HL), a neoplasm of predominantly B cell origin. Immunohistochemistry performed on 5-μm thick FFPE sections revealed expression of PRLR in HRS cells. Cellular immunofluorescence experiments showed that the HL-derived cell lines, Hs445, KMH2 and L428 overexpressed PRLR. The PRLR immunofluorescent signal was depleted after treating the cell lines with 10 …

Trust: Assessing The Efficacy Of An Intervention To Increase Hiv Self‑Testing Among Young Black Men Who Have Sex With Men (Msm) And Transwomen, Victoria Frye, Vijay Nandi, Mark Q. Paige, Jermaine Mccrossin, Debbie Lucy, Marya Gwadz, Patrick S. Sullivan, Donald R. Hoover, Leo Wilton

Publications and Research

HIV testing among young Black MSM and transwomen (YBMSM/TW) is the gateway to biomedical HIV prevention or treatment. HIV self-testing (HST) is a method that may increase consistent HIV testing. TRUST, a brief, peer-based behavioral intervention, was designed to increase uptake of consistent (every three months) HST among YBMSM/TW in New York City. To test the efficacy of the intervention, we randomized 200 friend pairs into either the intervention condition (TRUST) or a time and attention control condition. A modified intent-to-treat analysis found that self-reported HST at 3-month follow-up was statistically significantly higher (uOR 2.29; 95% CI 1.15, 4.58) and …

Microbiomes For All, Theodore R. Muth, Avrom J. Caplan

Publications and Research

Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number …

Update On The Use Of Transcranial Electrical Brain Stimulation To Manage Acute And Chronic Covid-19 Symptoms, Giuseppina Pilloni, Marom Bikson, Bashar W. Badran, Mark S. George, Steven A. Kautz, Alexandre Hideki Okano, Abrahão Fontes Baptista, Leigh E. Charvet

Publications and Research

The coronavirus disease 19 (COVID-19) pandemic has resulted in the urgent need to develop and deploy treatment approaches that can minimize mortality and morbidity. As infection, resulting illness, and the often prolonged recovery period continue to be characterized, therapeutic roles for transcranial electrical stimulation (tES) have emerged as promising non-pharmacological interventions. tES techniques have established therapeutic potential for managing a range of conditions relevant to COVID-19 illness and recovery, and may further be relevant for the general management of increased mental health problems during this time. Furthermore, these tES techniques can be inexpensive, portable, and allow for trained self-administration. Here, …