Digital Commons Network^™

Cov Genome Tracker: Tracing Genomic Footprints Of Covid-19 Pandemic, Saymon Akther, Edgaras Bezrucenkovas, Brian Sulkow, Christopher Panlasigui, Li Li, Wei-Gang Qiu, Lia Di

Publications and Research

Genome sequences constitute the primary evidence on the origin and spread of the 2019-2020 Covid-19 pandemic. Rapid comparative analysis of coronavirus SARS-CoV-2 genomes is critical for disease control, outbreak forecasting, and developing clinical interventions. CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. We resolve the direction of mutations by using a bat-associated genome as outgroup. At a broader evolutionary time scale, a companion browser provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular …

Impact Of Meteorological Factors On The Covid-19 Transmission: A Multicity Study In China, Jiangtao Liu, Ji Zhou, Jinxi Yao, Xiuxia Zhang, Lanyu Li, Xiaocheng Xu, Xiaotao He, Bo Wang, Shihua Fu, Tingting Niu, Jun Yan, Yanjun Shi, Xiaowei Ren, Jingping Niu, Weihao Zhu, Sheng Li, Bin Luo, Kai Zhang

Publications and Research

The purpose of the present study is to explore the associations between novel coronavirus disease 2019 (COVID- 19) case counts and meteorological factors in 30 provincial capital cities of China. We compiled a daily dataset including confirmed case counts, ambient temperature (AT), diurnal temperature range (DTR), absolute humidity (AH) and migration scale index (MSI) for each city during the period of January 20th to March 2nd, 2020. First, we explored the associations between COVID-19 confirmed case counts, meteorological factors, and MSI using non-linear regression. Then, we conducted a two-stage analysis for 17 cities with more than 50 confirmed cases. In …

Biological Sex Influences Susceptibility To Acinetobacter Baumannii Pneumonia In Mice, Sílvia Pires, Adeline Peignier, Jeremy Seto, Davida S. Smyth, Dane Parker

Publications and Research

Acinetobacter baumannii (A. baumannii) is an extremely versatile multidrug-resistant pathogen with a very high mortality rate; therefore, it has become crucial to understand the host response during its infection. Given the importance of mice for modeling infection and their role in preclinical drug development, equal emphasis should be placed on the use of both sexes. Through our studies using a murine model of acute pneumonia with A. baumannii, we observed that female mice were more susceptible to infection. Likewise, treatment of male mice with estradiol increased their susceptibility to infection. Analysis of the airway compartment revealed enhanced inflammation and reduced …

Congenital Zika Syndrome - Background And Nutrition Care Of Affected Infants, Ann Gaba, Ghada Soliman

Publications and Research

This review provides a history and overview of Zika infection, with special attention to resultant birth defects and the nutrition care required by Zika affected infants.

C-Di-Gmp Modulates Type Iv Msha Pilus Retraction And Surface Attachment In Vibrio Cholerae, Kyle A. Floyd, Calvin K. Lee, Wujing Xian, Mahmoud Nametalla, Aneesa Valentine, Benjamin Crair, Shiwei Zhu, Hannah Q. Hughes, Jennifer L. Chlebek, Daniel C. Wu, Jin Hwan Park, Ali M. Farhat, Charles J. Lomba, Courtney K. Ellison, Yves V. Brun, Javier Campos-Gomez, Ankur B. Dalia, Jun Liu, Nicolas Biais, Gerard C. L. Wong, Fitnat H. Yildiz

Publications and Research

Biofilm formation by Vibrio cholerae facilitates environmental persistence, and hyperinfectivity within the host. Biofilm formation is regulated by 3’,5’-cyclic diguanylate (c-di-GMP) and requires production of the type IV mannose-sensitive hemagglutinin (MSHA) pilus. Here, we show that the MSHA pilus is a dynamic extendable and retractable system, and its activity is directly controlled by c-di-GMP. The interaction between c-di-GMP and the ATPase MshE promotes pilus extension, whereas low levels of c-di-GMP correlate with enhanced retrac- tion. Loss of retraction facilitated by the ATPase PilT increases near-surface roaming motility, and impairs initial surface attachment. However, prolonged retraction upon surface attach- ment results …

Paleopathological Research In Continental China: Introduction To The Special Section, Elizabeth Berger, Kate Pechenkina

Publications and Research

We set out to assemble this special issue of IJPP with three goals in mind: (1) to familiarize Anglophone readers with research on paleopathology conducted by Chinese scholars; (2) to enhance interest in paleopathological research among Chinese scholars, and to foster the use of differential diagnosis as the key mode of paleopathological analysis; and (3) to initiate integration of pathological analysis of human skeletal collections with historical records documenting early medical practices, epidemics, development and age-related diseases, and demographic records.

The collection of papers that follows present new data, from a range of time periods and geographic and social contexts, …

Transposon Mutagenesis In Mycobacterium Kansasii Links A Small Rna Gene To Colony Morphology And Biofilm Formation And Identifies 9,885 Intragenic Insertions That Do Not Compromise Colony Outgrowth, William C. Budell, Gabrielle A. Germain, Niklas Janisch, Zaid Mckie-Krisberg, Anitha D. Jayaprakash, Andrew E. Resnick, Luis E. N. Quadri

Publications and Research

Mycobacterium kansasii (Mk) is a resilient opportunistic human pathogen that causes tuberculosis-like chronic pulmonary disease and mortality stemming from comorbidities and treatment failure. The standard treatment of Mk infections requires costly, long-term, multidrug courses with adverse side effects. The emergence of drug-resistant isolates further complicates the already challenging drug therapy regimens and threatens to compromise the future control of Mk infections. Despite the increasingly recognized global burden of Mk infections, the biology of this opportunistic pathogen remains essentially unexplored. In particular, studies reporting gene function or generation of defined mutants are scarce. Moreover, no transposon (Tn) mutagenesis tool has been …

A Real-World Analysis Of Patient Characteristics And Predictors Of Hospitalization Among Us Medicare Beneficiaries With Respiratory Syncytial Virus Infection, Veronique Wyffels, Furaha Kariburyo, Sandra Gavart, Roman Fleischhackl, Huseyin Yuce

Publications and Research

Introduction: Little has been published on respiratory syncytial virus (RSV) among Medicare patients at high risk (HR) of RSV complications due to age or comorbidity. Methods: Adult patients (at least 18 years of age) with at least 1 diagnostic code for RSV were identified using the 5% US Medicare database from 2011 through 2015. Patients were required to have continuous health plan enrollment for 180 days pre- and 180 days post-RSV diagnosis (baseline and follow-up periods, respectively). HR was defined as diagnosis of chronic lung disease, congestive heart failure, or weakened immune system for 180 days during the base-line period. …

Leveraging Eelectronic Health Records To Develop Cardiovascular Risk Profiles For Primary Prevention With Youth Living With Hiv In Multidisciplinary Adolescent Hiv Care Settings, Sitaji Gurung

Dissertations and Theses

Background: HIV infection has shown to be associated with increased risk for, and earlier occurrence of cardiovascular disease (CVD). Emerging evidence suggests that detectable viral load (VL) and CD4 ≤ 200 contribute substantially to increased risk of CVD. Cigarette smoking is prevalent in at least 40% of those with HIV, and significantly more common compared to the general population. As many as 33% of adolescents are overweight, and this excess weight leads to lipid abnormalities, and increases in metabolic syndrome. With the newer formulation of antiretroviral therapy (ART) agents available as a component of single tablet regimens (STR), it is …

Mutational Analysis And Domain Characterization Of The Apolipoprotein L-1 Ion Channel, Charles M. Schaub

Dissertations, Theses, and Capstone Projects

The human innate immunity factor Apolipoprotein L-1 (APOL1) protects against Trypanosoma brucei brucei infection. Recent studies have shown recombinant APOL1 (rAPOL1) inserts into planar lipid bilayers at an acidic pH 5.6 and forms a cation-selective channel, which opens upon subsequent neutralization, pH 7.2. This corresponds with the pH changes APOL1 would encounter during endosome recycling, suggesting that APOL1 forms a pH-gated ion channel in the plasma membrane of the parasite, leading to uncontrolled ion flux and osmotic imbalance. However, structural and domain characteristics of the APOL1 channel are poorly understood, despite potential similarities to diphtheria and colicin toxins. Utilizing E. …

Through The Back Door: Proteins Escape Cells Without Conventional Permission, Michael J. Cohen

Dissertations, Theses, and Capstone Projects

Proteins secreted to the extracellular environment play a fundamental role as signals, in metabolism, and a variety of other processes. The process of secretion through the endoplasmic reticulum and Golgi to the plasma membrane is well documented, and all cargo in this pathway contains a signal peptide. However, a variety of proteins secreted from eukaryotes lack a signal peptide and are called unconventionally secreted proteins. Here we discuss known mechanisms of unconventional protein secretion, as well as model proteins which follow characterized pathways. Additionally, we summarize the roles various unconventionally secreted proteins play outside of cells and suggest criteria for …

Structure Of The Cell-Binding Component Of The Clostridium Difficile Binary Toxin Reveals A Di-Heptamer Macromolecular Assembly, Xingjian Xu, Raquel Godoy-Ruiz, Kaylin A. Adipietro, Christopher Peralta, Danya Ben-Hail, Kristeny M. Varney, Mary E. Cook, Braden M. Roth, Paul T. Wilder, Thomas Cleveland, Alexander Grishaev, Heather M. Neu, Sarah L. J. Michel, Wenbo Yu, Dorothy Beckett, Richard R. Rustand, Catherine Lancaster, John W. Loughney, Adam Kristopeit, Sianny Christantii, Jessica W. Olson, Alexander D. Mackerell, Amedee Des Georges, Edwin Pozharski, David J. Weber

Advanced Science Research Center

Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in addition to the enterotoxins TsdA and TsdB. The C. difficile toxin has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of singleparticle cryoelectron microscopy, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, 2 di-heptamer structures for activated CDTb (1.0 MDa) were solved at atomic resolution, including …

Protecting Public Health, Susan H. Davide, Christine Macarelli, Anty Lam

Publications and Research

In light of declining vaccination rates, oral health professionals need to be knowledgeable about current vaccine recommendations so they can best advise their patients and support public health.

Elucidation Of Putative Binding Partners For The Protein Encoded By Orf149 Of Cyprinid Herpesvirus 3 In Goldfish (Carassius Auratus), Simon Menanteau–Ledouble, Michael Gotesman, Ebrahim Razzazi‐Fazeli, Sven M. Bergmann, Mansour El‐Matbouli

Publications and Research

No abstract provided.

Antibacterial, Antifungal, Antioxidant Activity And Polyphenol Content Of Aerial Parts And Bulbs Of Allium Schugnanicum., Saidbeg Satorov, F. Mirzoeva, Sh. Kurbonbekova, Sh. Satorov, M. Vakhidova, Vyacheslav Dushenkov

Publications and Research

Objective: То study of antibacterial, antifungal and antioxidant activity, and content of polyphenols in the bulb and aerial parts of an endemic species of onion A. schugnanicum. Methods: An ethanol-based extract was prepared from fresh plants. Total polyphenolic content (Folin) and ABTS antioxidant capacity assays were used to characterized extracts. Extracts obtained from bulbs, peduncle, and seeds demonstrated antibacterial activity against the reference Staphylococcus aureus (ATCC 4929), Pseudomonas aeruginosa (ATCC 4930) and Klebsiella pneumoniae (ATCC 4927) strains, as well as against the hospital strains of the same types of bacteria, i.e. strains isolated from inpatient surgical patients. Results: The study …

Critical Issues In Health, Janet R. Heller

Open Educational Resources

This is a personal health course for today's college student. Topics cover basic information on mental health, nutrition, substance use disorder, violence prevention, chronic diseases, infectious diseases and reproductive health.

Contents include as OER reading list and a sample outline.

A revised syllabus was added on July 28, 2026. The changes were made to reflect more current information.

Pandemics And Methodological Developments In Epidemiology History, Alfredo Morabia

Publications and Research

No abstract provided.

Lps, A Tlr-4 Agonist And Viper A Tlr-4 Inhibitor Upregulate Phagocytosis Of Zymosan In Bv2 Cells, Sherouk Alzeory

Dissertations and Theses

Microglia cells are the first line of innate immunity defense in the central nervous system (CNS). They play a critical role in maintaining CNS homeostasis by having an active but yet balanced phagocytic activity. However, in various CNS related diseases, microglia cells have been shown to malfunction. In Alzheimer's Disease (AD), hyperactive microglia with impaired phagocytic activity is the main hallmark of this disease, along with the accumulation of amyloid-beta aggregates. Additionally, emerging new studies have suggested a fungal infection etiology to AD, specifically in relation to Candida albicans (C.albicans). Thus, understanding the mechanism of fungal clearance in the …

Dynamics And Phase Behavior Of Mixed Antibody-Excipient Adsorption At An Air/Water Interface, Ankit D. Kanthe

Dissertations and Theses

Monoclonal antibodies (mAbs) have become a leading candidate for oncological therapeutics due to their unparalleled selectivity. Monoclonal antibodies are amphiphilic, containing polar and nonpolar amino acid residues on their biomolecular surfaces. Their amphiphilic nature drives mAbs to strongly adsorb to air/water interfaces. Interfacial adsorption presents a central problem to the production and use of antibody-based pharmaceuticals. Air/water interfaces are frequently generated during the manufacture (filtration and chromatography) and production (freezing, thawing, filtration and filling) of the drug product. Moreover, air/water interfaces are present during the storage, transportation and administration of the therapeutics. When an air/water interface is created, the antibodies …

Hijacking The Fusion Complex Of Human Parainfluenza Virus As An Antiviral Strategy, T. C. Marcink, E. Yariv, K. Rybkina, V. Más, F. T. Bovier, A. Des Georges, A. L. Greninger, C. A. Alabi, M. Porotto, N. Ben-Tal, A. Moscona

Advanced Science Research Center

The receptor binding protein of parainfluenza virus, hemagglutinin- neuraminidase (HN), is responsible for actively triggering the viral fusion protein (F) to undergo a conformational change leading to insertion into the target cell and fusion of the virus with the target cell membrane. For proper viral entry to occur, this process must occur when HN is engaged with host cell receptors at the cell surface. It is possible to interfere with this process through premature activation of the F protein, distant from the target cell receptor. Conformational changes in the F protein and adoption of the postfusion form of the protein …

Leveraging Technology To Blend Large-Scale Epidemiologic Surveillance With Social And Behavioral Science Methods: Successes, Challenges, And Lessons Learned Implementing The Unite Longitudinal Cohort Study Of Hiv Risk Factors Among Sexual Minority Men In The United States, H. Jonathon Rendina, Ali J. Talan, Nicola F. Tavella, Jonathan Lopez Matos, Ruben H. Jimenez, S. Scott Jones, Brian Salfas, Drew Westmoreland

Publications and Research

The use of digital technologies to conduct large-scale research with limited interaction (i.e., no in-person contact) and objective endpoints (i.e., biological testing) has significant potential for the field of epidemiology, but limited research to date has been published on the successes and challenges of such approaches. We analyzed data from a cohort study of sexual minority men across the United States, collected using digital strategies during a 10-month period from 2017 to 2018. Overall, 113,874 individuals were screened, of whom 26,000 were invited to the study, 10,691 joined the study, and 7,957 completed all enrollment steps, including return of a …

High Tech, High Risk: Tech Ethics Lessons For The Covid-19 Pandemic Response, Emanuel Moss, Jacob Metcalf

Publications and Research

The COVID-19 pandemic has, in a matter of a few short months, drastically reshaped society around the world. Because of the growing perception of machine learning as a technology capable of addressing large problems at scale, machine learning applications have been seen as desirable interventions in mitigating the risks of the pandemic disease. However, machine learning, like many tools of technocratic governance, is deeply implicated in the social production and distribution of risk and the role of machine learning in the production of risk must be considered as engineers and other technologists develop tools for the current crisis. This paper …

Community-Based Responses To Negative Health Impacts Of Sexual Humanitarian Anti-Trafficking Policies And The Criminalization Of Sex Work And Migration In The Us, Heidi Hoefinger, Jennifer Musto, P.G. Macioti, Anne E. Fehrenbacher, Nicola Mai, Calum Bennachie, Calogero Giametta

Publications and Research

System-involvement resulting from anti-trafficking interventions and the criminalization of sex work and migration results in negative health impacts on sex workers, migrants, and people with trafficking experiences. Due to their stigmatized status, sex workers and people with trafficking experiences often struggle to access affordable, unbiased, and supportive health care. This paper will use thematic analysis of qualitative data from in-depth interviews and ethnographic fieldwork with 50 migrant sex workers and trafficked persons, as well as 20 key informants from legal and social services, in New York and Los Angeles. It will highlight the work of trans-specific and sex worker-led initiatives …

An Overview Of The Health Delivery System In The State Of Mississippi, Cerlyn K. Ellis

Publications and Research

Imagine residing in a high-income country that doesn’t provide access to necessary healthcare. The state of Mississippi remains one of the poorest states in the United States. This has resulted in poor health outcomes and chronic access barriers. Residents of Mississippi ranks poorly in most health indicators, including Infectious Disease, Infant Mortality, Clinic Care, Obesity, Diabetes, and Premature Death.

With half of all rural hospitals in Mississippi threatened with closure, access and quality of care barriers will become more challenging to resolve. This comes partly as a result of the state largely governed by Republicans and the legislators refusing to …

Hiv Prevention Via Mobile Messaging For Men Who Have Sex With Men (M-Cubed): Protocol For A Randomized Controlled Trial, Patrick Sean Sullivan, Ryan J. Zahn, Sarah Wiatrek, Cristian J. Chandler, Sabina Hirshfield, Rob Stephenson, Jose A. Bauermeister, Mary Ann Chiasson, Martin J. Downing, Deborah J. Gelaude, Aaron J. Siegler, Keith Horvath, Erin Rogers, Ana Alas, Evelyn J. Olansky, Heather Saul, Eli S. Rosenberg, Gordon Mansergh

Publications and Research

Background:

Men who have sex with men (MSM) continue to be the predominately impacted risk group in the United States HIV epidemic and are a priority group for risk reduction in national strategic goals for HIV prevention. Modeling studies have demonstrated that a comprehensive package of status-tailored HIV prevention and care interventions have the potential to substantially reduce new infections among MSM. However, uptake of basic prevention services, including HIV testing, sexually transmitted infection (STI) testing, condom distribution, condom-compatible lubricant distribution, and preexposure prophylaxis (PrEP), is suboptimal. Further, stronger public health strategies are needed to promote engagement in HIV care …

From The Human To The Planetary: Speculative Futures Of Care, Miriam Ticktin

Publications and Research

This is largely a theoretical, speculative essay that takes on the question of what ‘care’ looks like at a moment when climate change is increasingly taking center stage in public and political discussions. Starting with two new practices, namely, humanitarian care for nonhumans and One Health collaborations, I seek to determine what forms of political care can incorporate the well-being of future generations and future iterations of the earth. After an exploration of One Health as an approach to planetary care, I ask what its parts enable us to think, despite its limitations; I focus on the new human-nonhuman assemblages …

Hypertension And Hiv In An Urban Slum Setting, Port-Au-Prince, Haiti, Olga Tymejczyk

Dissertations and Theses

Background: Rapidly growing urban slum settings increasingly face co-occurring communicable and non-communicable health crises, against the backdrop of extreme poverty, and social and environmental vulnerability. In Haiti, sparse data suggest a growing burden of hypertension and cardiovascular disease (CVD), along with substantial prevalence of HIV, increasingly recognized as a major CVD risk factor. As life-saving antiretroviral treatment (ART) is extended to more people living with HIV (PLWH), their risk of CVD increases with longer life expectancy and possibly cumulative ART exposure. Pregnant HIV-positive women may face additional cardiovascular vulnerability, due to the risk of gestational hypertension and pre-eclampsia. Integration of …

Trends In The Timeliness Of Hiv Diagnosis And Antiretroviral Treatment Initiation Before, During And After The “Treat All” Recommendation – New York City, 2006 - 2015, Mckaylee Robertson

Dissertations and Theses

BACKGROUND: Voluntary HIV testing followed by immediate antiretroviral treatment (ART) initiation (universal testing and treatment) has become an integral part of strategies to eliminate HIV and control the HIV/AIDS epidemic. Minimizing the time from HIV infection to ART initiation is essential for universal test and treatment to be optimally effective. In New York City, an epicenter of the HIV epidemic, the ‘treat all’ recommendation, immediate treatment for all people diagnosed with HIV, was made in late 2011, and efforts to ‘treat all’ were contemporaneous with large scale HIV testing initiatives in NYC. The overarching goal of this dissertation was to …

Classified Information: The Newsletter Of The Lloyd Sealy Library, Lloyd Sealy Library, Cuny John Jay College Of Criminal Justice

Reports and Publications from John Jay College

Classified Information was a publication that informed the College about Library services, personnel, upcoming events, new technologies, and available resources.

Innate Antibodies, Murine Models, And Evolution: A Study Of Trypanosome Lytic Factor Functions And Their Translational Applications, Joseph P. Verdi

Dissertations, Theses, and Capstone Projects

Trypanosome lytic factors (TLFs) are primate-specific antimicrobial protein complexes that lyse African trypanosome parasites by delivering the channel-forming toxin APOL1 to the invading microorganisms. Human serum contains two TLFs that are delivered to the parasite by separate mechanisms, only one of which has been characterized. TLF1 is endocytosed by a receptor that is typically blocked by other serum factors in vivo, suggesting that TLF2 is the more relevant lytic factor in the context of trypanosome immunity. TLF2 is non-covalently associated with polyclonal immunoglobulin M (IgM) antibodies, which we report here to be involved in the uptake mechanism. The TLF2-IgMs …