Prophylactic Bacteriophage Administration More Effective Than Post-Infection Administration In Reducing Salmonella Enterica Serovar Enteritidis Shedding In Quail, Mosab Ahmadi, M. Amir Karimi Torshizi, Shaban Rahimi, John J. Dennehy

Publications and Research

Infections caused by Salmonella bacteria, often through poultry products, are a serious public health issue. Because of drawbacks associated with antibiotic prophylaxis, alternative treatments are sought. Bacterial viruses (bacteriophages) may provide an effective alternative, but concerns remain with respect to bacteriophage stability and effectiveness. To this end, we assessed the stability of a novel bacteriophage isolated from poultry excreta, siphovirus PSE, and its effectiveness in reducing Salmonella enterica serovar Enteritidis colonization in vitro and in vivo. Moreover, we sought to determine how the timing (prophylactic or therapeutic) and route (oral gavage or vent lip) of PSE administration impacted its effectiveness. …

Cultivating Minority Scientists: Undergraduate Research Increases Self-Efficacy And Career Ambitions For Underrepresented Students In Stem, Anthony Carpi, Darcy M. Ronan, Heather M. Falconer, Nathan H. Lents

Publications and Research

In this study, Social Cognitive Career Theory (SCCT) is used to explore changes in the career intentions of students in an undergraduate research experience (URE) program at a large public minority-serving college. Our URE model addresses the challenges of establishing an undergraduate research program within an urban, commuter, underfunded, Minority-Serving Institution (MSI). However, our model reaches beyond a focus on retention and remediation toward scholarly contributions and shifted career aspirations. From a student’s first days at the College to beyond their graduation, we have encouraged them to explore their own potential as scientists in a coordinated, sequential, and self-reflective process. …

Machine Learning Meta-Analysis Of Large Metagenomic Datasets: Tools And Biological Insight, Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata

Publications and Research

Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction …

Untangling The Relationship Between Antiretroviral Therapy Use And Incident Pregnancy: A Marginal Structural Model Analysis Using Data From 47,313 Hiv-Positive Women In East Africa, Batya Elul, Kara K. Wools-Kaloustian, Yingfeng Wu, Beverly S. Musick, Harriet Nuwagaba-Biribonwoha, Denis Nash, Samuel Ayaya, Elizabeth Bukusi, Pius Okong, Juliana Otieno, Deo Wabwire, Andrew Kambugu, Constantin T. Yiannoutsos

Publications and Research

Background: Scale-up of triple-drug antiretroviral therapy (ART) in Africa has transformed the context of childbearing for HIV-positive women and may impact pregnancy incidence in HIV programs.

Methods: Using observational data from 47,313 HIV-positive women enrolled at 26 HIV clinics in Kenya and Uganda between 2001 and 2009, we calculated the crude cumulative incidence of pregnancy for the pre-ART and on-ART periods. The causal effect of ART use on incident pregnancy was assessed using inverse probability weighted marginal structural models, and the relationship was further explored in multivariable Cox models.

Results: Crude cumulative pregnancy incidence at 1 year after enrollment/ART initiation …

Pharmacologic Inhibition Of Host Phosphodiesterase-4 Improves Isoniazid-Mediated Clearance Of Mycobacterium Tuberculosis, Selvakumar Subbian, Mi-Sun Koo, Liana Tsenova, Vikram Khetani, Jerome B. Zeldis, Dorothy Fallows, Gilla Kaplan

Publications and Research

The lengthy duration of multidrug therapy needed to cure tuberculosis (TB) poses significant challenges for global control of the disease. Moreover, chronic inflammation associated with TB leads to pulmonary damage that can remain even after successful cure. Thus, there is a great need for the development of effective shorter drug regimens to improve clinical outcome and strengthen TB control. Host-directed therapy (HDT) is emerging as a novel adjunctive strategy to enhance the efficacy and shorten the duration of TB treatment. Previously, we showed that the administration of CC-3052, a phosphodiesterase-4 inhibitor (PDE4i), reduced the host inflammatory response during Mycobacterium tuberculosis …

Developing A Video-Based Ehealth Intervention For Hiv-Positive Gay, Bisexual, And Other Men Who Have Sex With Men: Study Protocol For A Randomized Controlled Trial, Sabina Hirshfield, Martin J. Downing Jr., Jeffrey T. Parsons, Christina Grov, Rachel J. Gordon, Steven T. Houang, Roberta Scheinmann, Patrick S. Sullivan, Irene S. Yoon, Ian Anderson, Mary Ann Chiasson

Publications and Research

Background: Gay, bisexual, and other men who have sex with men (GBMSM) accounted for 67% of new US human immunodeficiency virus (HIV) infections in 2012; however, less than 40% of HIV-positive GBMSM are virally suppressed. Preventing transmission from virally unsuppressed men who have condomless anal sex (CAS) with serodiscordant partners is a public health imperative. New HIV infections in GBMSM are attributed in part to online access to sex partners; therefore, low-cost eHealth interventions are a unique opportunity to reach men where they meet partners.

Objective: To describe the protocol of a randomized controlled trial evaluating whether video-based messaging delivered …

Effect Of Cntf Derived Peptide, P021 On Cognition And Pathology In 3xtg-Ad Mouse Model Of Alzheimer's Disease, Narjes Baazaoui

Dissertations, Theses, and Capstone Projects

Studies described in this thesis deal with the preventive effects of a neurogenic/neurotropic peptidergic compound, P021, on neurogenesis and synaptic deficits, neurodegeneration, cognitive impairment, and Ab and tau pathologies in a 3xTg-AD mouse model of Alzheimer’s disease (AD).

Background: AD is a chronic progressive neurodegenerative disease. Its multifactorial nature and the heterogeneity make its treatment especially challenging. Although it is a major burden in society, at present there is no drug that can stop or slow down the progression of the disease. Currently, the only available treatments are symptomatic and for mild to severe stages. The development of a drug …

Stochastic Processes And Their Applications To Change Point Detection Problems, Heng Yang

Dissertations, Theses, and Capstone Projects

This dissertation addresses the change point detection problem when either the post-change distribution has uncertainty or the post-change distribution is time inhomogeneous. In the case of post-change distribution uncertainty, attention is drawn to the construction of a family of composite stopping times. It is shown that the proposed composite stopping time has third order optimality in the detection problem with Wiener observations and also provides information to distinguish the different values of post-change drift. In the case of post-change distribution uncertainty, a computationally efficient decision rule with low-complexity based on Cumulative Sum (CUSUM) algorithm is also introduced. In the time …

Biosynthesis And Roles Of Virulence Conferring Cell Wall Associated Dimycocerosate Esters In Mycobacterium Marinum, Poornima Mohandas

Dissertations, Theses, and Capstone Projects

Mycobacterial species include a variety of obligate and opportunistic pathogens that cause several important diseases affecting mankind such as tuberculosis and leprosy. The most unique feature of these bacteria is their intricate cell wall that poses a permeability barrier to antibiotics and contributes to their pathogenicity and persistence within the host. The cell wall hosts several complex lipids such as dimycocerosate esters (DIMs), which are found in many clinically relevant pathogenic species of mycobacteria. DIMs have been implicated in the virulence of mycobacteria and play a major role in helping the bacteria evade host immune responses. It is therefore crucial …

Mechanism Of Action And Applications Of Interleukin 24 In Immunotherapy, Leah Persaud, Dayenny De Jesus, Oliver Brannigan, Maria Richiez-Paredes, Jeannette Huaman, Giselle Alvarado, Linda Riker, Gissete Mendez, Jordan Dejoie, Moira Sauane

Publications and Research

Interleukin 24 (IL-24) is an important pleiotropic immunoregulatory cytokine, whose gene is located in human chromosome 1q32-33. IL-24’s signaling pathways have diverse biological functions related to cell differentiation, proliferation, development, apoptosis, and inflammation, placing it at the center of an active area of research. IL-24 is well known for its apoptotic effect in cancer cells while having no such effect on normal cells. IL-24 can also be secreted by both immune and non-immune cells. Downstream effects of IL-24, after binding to the IL-20 receptor, can occur dependently or independently of the JAK/STAT signal transduction pathway, which is classically involved in …

Brainstorming Solutions For The Unintended Consequences Of Antibiotics And The Development Of Resistant Bacteria, Rajini D. Ramsukh

Dissertations, Theses, and Capstone Projects

This thesis entails the study of bacteria that cause infections requiring antibiotic treatments and the development of antibiotic resistance as an unintended consequence. Antibiotics were originally formulated to remedy medical problems, but the consequence of inappropriate usage has created a serious setback: the development of drug-resistant bacteria. The objective of this thesis is to illuminate the misuse, over-prescription, and mis-monitoring of the dispensing of antibiotics that results in the development of antibiotic-resistant bacteria. However, the core of the thesis is to evaluate the solutions implemented thus far to remedy the already existing problem of resistant bacteria and to propose suggestions …

P2x7r-Panx1 Complex Impairs Bone Mechanosignaling Under High Glucose Levels Associated With Type-1 Diabetes, Zeynep Seref-Ferlengez, Stephanie Maung, Mitchell B. Schaffler, David C. Spray, Sylvia O. Suadicani, Mia M. Thi

Publications and Research

Type 1 diabetes (T1D) causes a range of skeletal problems, including reduced bone density and increased risk for bone fractures. However, mechanisms underlying skeletal complications in diabetes are still not well understood.We hypothesize that high glucose levels in T1D alters expression and function of purinergic receptors (P2Rs) and pannexin 1 (Panx1) channels, and thereby impairs ATP signaling that is essential for proper bone response to mechanical loading and maintenance of skeletal integrity. We first established a key role for P2X7 receptor-Panx1 in osteocyte mechanosignaling by showing that these proteins are co-expressed to provide a major pathway for flow-induced ATP release. …

College Senate Minutes May 12, 2016, Bronx Community College Senate

BCC Governance Archives

Minutes for the meeting of the College Senate on May 12, 2016.

Wsq: Survival Editor's Note, Cynthia Chris, Matt Brim

Publications and Research

This Editor's Note introduces the WSQ issue "Survival," co-edited by Taylor Black, Elena Glasberg, and Frances Bartkowski, which explores affirmative acts of survival in the face of illness, occupation, violence, and environmental crises.

Awareness Of Rabies And Response To Dog Bites In A Bangladesh Community, Sumon Ghosh, Sukanta Chowdhury, Najmul Haider, Rajub K. Bhowmik, Md. S. Rana, Aung S. Prue Marma, Muhammad B. Hossain, Nitish C. Debnath, Be-Nazir Ahmed

Publications and Research

Community awareness regarding rabies and treatment seeking behaviours are critical both for the prevention and control of the disease in human and animals. We conducted a study to explore people’s awareness about rabies, their attitudes towards dogs and practices associated with treating dog bites in Satkhira Sadar, a southwestern sub-district of Bangladesh. Of the total 3200 households (HHs) surveyed, the majority of the respondents have heard about rabies (73%) and there was a high level of awareness that dog bite is the main cause of rabies (86%), and that rabies can be prevented by vaccination (85%). However, 59% of the …

Dengue-Induced Autophagy, Virus Replication And Protection From Cell Death Require Er Stress (Perk) Pathway Activation, E. Datan, S. G. Roy, G. Germain, N. Zali, J. E. Mclean, G. Golshan, S. Harbajan, R. A. Lockshin, Z. Zakeri

Publications and Research

Avirus that reproduces in a host without killing cells can easily establish a successful infection. Previously, we showed that dengue-2, a virus that threatens 40% of the world, induces autophagy, enabling dengue to reproduce in cells without triggering cell death. Autophagy further protects the virus-laden cells from further insults. In this study, we evaluate how it does so; we show that dengue upregulates host pathways that increase autophagy, namely endoplasmic reticulum (ER) stress and ataxia telangiectasiamutated (ATM) signaling followed by production of reactive oxygen species (ROS). Inhibition of ER stress or ATM signaling abrogates the dengueconferred protection against other cell …

Layer-Switching Cost And Optimality In Information Spreading On Multiplex Networks, Byungjoon Min, Sang-Hwan Gwak, Nanoom Lee, K. I. Goh

Publications and Research

We study a model of information spreading on multiplex networks, in which agents interact through multiple interaction channels (layers), say online vs. offline communication layers, subject to layerswitching cost for transmissions across different interaction layers. The model is characterized by the layer-wise path-dependent transmissibility over a contact, that is dynamically determined dependently on both incoming and outgoing transmission layers. We formulate an analytical framework to deal with such path-dependent transmissibility and demonstrate the nontrivial interplay between the multiplexity and spreading dynamics, including optimality. It is shown that the epidemic threshold and prevalence respond to the layer-switching cost non-monotonically and that …

Drug Repurposing To Target Ebola Virus Replication And Virulence Using Structural Systems Pharmacology, Zheng Zhao, Che Martin, Raymond Fan, Philip E. Bourne, Lei Xie

Publications and Research

Background: The recent outbreak of Ebola has been cited as the largest in history. Despite this global health crisis, few drugs are available to efficiently treat Ebola infections. Drug repurposing provides a potentially efficient solution to accelerating the development of therapeutic approaches in response to Ebola outbreak. To identify such candidates, we use an integrated structural systems pharmacology pipeline which combines proteome-scale ligand binding site comparison, protein-ligand docking, and Molecular Dynamics (MD) simulation.

Results: One thousand seven hundred and sixty-six FDA-approved drugs and 259 experimental drugs were screened to identify those with the potential to inhibit the replication and virulence …

Sexual Behavior Varies Between Same-Race And Different-Race Partnerships: A Daily Diary Study Of Highly Sexually Active Black, Latino, And White Gay And Bisexual Men, Christian Grov, Demetria Cain, H. Jonathan Rendina, Ana Ventuneac, Jeffrey T. Parsons

Publications and Research

Background. Gay and bisexual men (GBM) are at elevated risk for gonorrhea and chlamydia trachomatis (GC/CT). Rectal GC/CT symptoms may be less obvious than urethral, increasing opportunities for undiagnosed rectal GC/CT.

Method. A U.S. national sample of 1,071 GBM completed urethral and rectal GC/CT testing and an online survey.

Results. In total, 6.2% were GC/CT positive (5.3% rectal, 1.7% urethral). We calculated adjusted (for education, race, age, relationship status, having health insurance, and income) odds ratios for factors associated with rectal and urethral GC/CT diagnoses. Age was inversely associated with urethral and rectal GC/CT. Compared to White men, Latinos had …

Genome Assembly And Geospatial Phylogenomics Of The Bed Bug Cimex Lectularius, Jeffrey A. Rosenfeld, Darryl Reeves, Mercer R. Brugler, Apurva Narechania, Sabrina Simon, Russell Durrett, Jonathan Foox, Kevin Shianna, Michael C. Schatz, Jorge Gandara, Ebrahim Afshinnekoo, Ernest T. Lam, Alex R. Hastie, Saki Chan, Han Cao, Michael Saghbini, Alex Kentsis, Paul J. Planet, Vladyslav Kholodovych, Michael Tessler, Richard Baker, Rob Desalle, Louis N. Sorkin, Sergios-Orestis Kolokotronis, Mark E. Siddall, George Amato, Christopher E. Mason

Publications and Research

The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug’s basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding and noncoding gene models. The most pronounced change in gene expression during the life cycle occurs after feeding on …

The Evolution Of The Viral Rna Sensor Oas1 In Old World Monkeys And Cetartiodactyls, Ian Fish

Dissertations, Theses, and Capstone Projects

Animals produce an array of sensors patrolling the intracellular environment poised to detect and respond to viral infection. The oligoadenylate synthetase family of enzymes comprises a crucial part of this innate immune response, directly signaling endonuclease activity responsible for inhibiting viral replication. Oligoadenylate synthetase 1 plays a vital role in animal susceptibility to pathogens including flaviviruses such as dengue, West Nile, and hepatitis c virus. This thesis includes a population level analysis of OAS1 diversity within macaque and baboon species followed by a broader survey of the gene in nineteen Old World monkeys. My research found that at the species …

Multilevel Analysis Of Individual, Neighborhood, And Health Care Facility Characteristics Associated With Achievement And Maintenance Of Hiv Viral Suppression Among Persons Newly Diagnosed With Hiv In New York City, Ellen W. Wiewel

Dissertations, Theses, and Capstone Projects

Objective

To investigate the effect of individual, health care facility, and neighborhood characteristics on achievement and maintenance of HIV viral suppression, among New York City residents aged 13 years and older diagnosed with HIV between 2006 and 2012.

Methods

I used individual-level data from the New York City HIV surveillance registry and Case Surveillance-Based Sampling, facility-level data from the surveillance registry, and neighborhood-level data from the U.S. Census and American Community Survey. The outcomes of interest were first viral suppression after diagnosis (Aims 1 and 3; ≤400 copies/mL) and virologic failure after first suppression among persons who achieved suppression (Aim …

The Impact Of Climate Variability And Conflict On Childhood Diarrhea And Malnutrition In West Africa, Gillian Dunn

Dissertations, Theses, and Capstone Projects

Objectives: This dissertation aims to contribute to our understanding of how climate variability and armed conflict impacts diarrheal disease and malnutrition among young children in West Africa. Two studies examine the associations between climate and diarrheal disease across the whole study area – ten countries in West Africa during the period 2008-2013. The third study examines diarrheal disease and malnutrition in Northeast Nigeria before (2008) and after (2013) the start of the current armed conflict in the area.

Methods: Outcome variables and child, caregiver, and household characteristics for these studies are from the Demographic and Health Surveys. Additional datasets include …

Adjunctive Phosphodiesterase-4 Inhibitor Therapy Improves Antibiotic Response To Pulmonary Tuberculosis In A Rabbit Model, Selvakumar Subbian, Liana Tsenova, Jennifer Holloway, Blas Peixoto, Paul O'Brien, Veronique Dartois, Vikram Khetani, Jerome B. Zeldis, Gilla Kaplan

Publications and Research

Objectives: Adjunctive host-directed therapy is emerging as a new potential approach to improve the outcome of conventional antimicrobial treatment for tuberculosis (TB).We tested the ability of a phosphodiesterase-4 inhibitor (PDE4i) CC-11050, co-administered with the first-line anti-TB drug isoniazid (INH), to accelerate bacillary killing and reduce chronic inflammation in the lungs of rabbits with experimental Mycobacterium tuberculosis (Mtb) infection.

Methods: A rabbit model of pulmonary TB that recapitulates the pathologic manifestations seen in humans was used. Rabbits were infected with virulent Mtb by aerosol exposure and treated for eight weeks with INH with orwithout CC-11050, starting at fourweeks post infection. The …

Killer-Cell Immunoglobulin-Like Receptor (Kir) Gene Profiles Modify Hiv Disease Course, Not Hiv Acquisition In South African Women, V. Naranbhai, D. De Assis Rosa, L. Werner, R. Moodley, H. Hong, A. Kharsany, K. Mlisana, S. Sibeko, N. Garrett, D. Chopera, William H. Carr, Q. Abdool Karim, A. V. S. Hill, S. S. Abdool Karim, M. Altfeld, C. M. Gray, T. Ndung’U

Publications and Research

Background: Killer-cell Immunoglobulin-like Receptors(KIR) interact with Human Leukocyte Antigen(HLA) to modify natural killer- and T-cell function. KIR are implicated in HIV acquisition by small studies that have not been widely replicated. A role for KIR in HIV disease progression is more widely replicated and supported by functional studies.

Methods: To assess the role of KIR and KIR ligands in HIV acquisition and disease course, we studied at-risk women in South Africa between 2004–2010. Logistic regression was used for nested case–control analysis of 154 women who acquired vs. 155 who did not acquire HIV, despite high exposure. Linear mixed-effects models were …

Maternal Mortality: A Policy Comparison Between Nigeria And India., Rachel Quarles

Dissertations and Theses

A staggering number of women die from preventable deaths each year from causes related to pregnancy and childbirth. India hosts the greatest number of actual maternal deaths in the world, although Nigeria’s ratio of maternal deaths to live births is greater than India’s. This thesis focuses on the experience of these two countries in order to determine if India’s governmental policies, level of government corruption, and traditional practices directly lead to its comparably better maternal health statistics. India has demonstrated lower ratios of maternal mortality and more consistent improvement in maternal health indicators than Nigeria as a result of stronger …

Knowledge-Based Tweet Classification For Disease Sentiment Monitoring, Xiang Ji, Soon Ae Chun, James Geller

Publications and Research

Disease monitoring and tracking is of tremendous value, not only for containing the spread of contagious diseases but also for avoiding unnecessary public concerns and even panic. In this chapter, we present a near real-time sentiment analysis service of public health-related tweets. Traditionally, it is impossible for humans to effectively measure the degree of public health concerns due to limited resources and significant time delays. To solve this problem, we have developed a computational intelligence approach for Epidemic Sentiment Monitoring System (ESMOS) to automatically analyze the disease sentiments and gauge the Measure of Concern (MOC) expressed by Twitter users. More …

"Sociocultural Predictors Of Risky Sexual Behaviors: 1 The Role Of Nativity Status, Race, Ethnic Identity And Self-Construal", Elvine B. Andjembe

Dissertations and Theses

Recent national health reports have shown that despite a considerable increase in sexual health knowledge, risky sexual behaviors’ rates among the youth are on the rise. Minorities are disproportionately affected, which translates into strong racial disparities in health outcomes such as STI/STDs, and HIV prevalence. The literature examining ethnic differences in health behaviors has studied ethnic identity (self-identification with and commitment to the values of one’s ethnic group) as a protective factor against an array of maladaptive behaviors. In addition, self-construal, which refers to the extent to which one is individualistic or collectivistic has also been established as a positive …

Globalization, Tourism And Sustainable Development: The Multifaceted Impact Of Tourism On Development And Poverty Alleviation In Brazil, Gaëlle Lopes Saraiva

Dissertations and Theses

Globalization is a popular concept deeply embedded in our era that represents the widespread intensification of transnational connections emblematic of this century. In general, this study aims to clarify the contradictory effects globalization exerts on development by specifically analyzing the particular impact of tourism in the emerging economy of Brazil. It is argued that the unequal distribution of tourism activities between urban and rural areas, and the prevalence of specific sizes and types of tourism are the main factors involved in sustaining unequal patterns of development across the country. The study concludes that public-private partnerships in tourism should prioritize the …

How N.Y.’S Biggest For-Profit Nursing Home Group Flourishes Despite A Record Of Patient Harm, Jennifer Lehman

Capstones

How N.Y.'s Biggest For-Profit Nursing Home Group Flourishes Despite a Record of Patient Harm

The state’s “character-and-competence” reviews are supposed to weed out operators with histories of violations and fines— but regulators don’t always act on the full story.