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 …

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 …

Implementing Information Literacy (Il) Into Stem Writing Courses: Effect Of Il Instruction On Students’ Writing Projects At An Urban Community College, Miseon Kim, Mercedes Franco, Dugwon Seo

Publications and Research

The purpose of this study was to implement information literacy (IL) into Science, Technology, Engineering, and Mathematics (STEM) writing courses at an urban community college, investigate if students’ information literacy (IL) skills were improved through library one-shot instruction, and determine if there was an association between IL skills and students’ writing performance. Students in the experimental group attended the library instructional class and students in the control group had no library class. Students’ research papers were scored using the Association of American Colleges & Universities (AAC&U) Information Literacy VALUE Rubric to grade the effectiveness of the library instruction (Association …

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.

The White Album As Neo-Victorian Fiction Of Loss, Lucas Kwong

Publications and Research

Although much has been written about the Beatles' celebration of Victorian culture on the album Sgt. Pepper's Lonely Hearts Club Band, little scholarship, if any, has focused on the White Album’s relationship to the late Victorian period. This paper examines the White Album through the lens of what Victorian studies scholar Stephen Arata has called “fictions of loss,” a body of late Victorian texts depicting intertwined processes of “national, biological, [and] aesthetic” decline. Through examining songs like "Helter Skelter" and "Revolution Number 9," I argue that the White Album deserves consideration alongside Dracula and She as a “fiction of loss,” …

The Ends Of Medicine And The Experience Of Patients, D. Robert Macdougall

Publications and Research

The ends of medicine are sometimes construed simply as promotion of health, treatment and prevention of disease, and alleviation of pain. Practitioners might agree that this simple formulation captures much of what medical practice is about. But while the ends of medicine may seem simple or even obvious, the essays in this issue demonstrate the wide variety of philosophical questions and issues associated with the ends of medicine. They raise questions about how to characterize terms like “health” and “disease”; whether medicine’s goals should be extended to include enhancement beyond normal human function; and whether the ends of medicine are …

Molecular Dynamics Of Mutated Dna Structures And The Effect On Surrounding Water Molecules, Christina Bhawanidin, Ashley Santos, Ivan Melo

Publications and Research

The process of repairing damaged bases in DNA molecules plays an important role in maintaining the information stored in DNA. We believe that there are two factors may facilitate the recognition of a mutation. The first is the structural changes in the DNA, the second is the changes in the thermodynamic properties of the water surrounding the DNA. Here we investigated the effects of a Uracil‐Guanine mispair on the structure of the DNA as well as its effect on the static and dynamic properties of the surrounding water molecules. We performed molecular dynamic simulations of the mutated and non mutated …

A Micro-Optic Stalk (Muos) System To Model The Collective Migration Of Retinal Neuroblasts, Stephanie Zhang, Miles Markey, Caroline D. Pena, Tadmiri Venkatesh, Maribel Vasquez

Publications and Research

Contemporary regenerative therapies have introduced stem-like cells to replace damaged neurons in the visual system by recapitulating critical processes of eye development. The collective migration of neural stem cells is fundamental to retinogenesis and has been exceptionally well-studied using the fruit fly model of Drosophila Melanogaster. However, the migratory behavior of its retinal neuroblasts (RNBs) has been surprisingly understudied, despite being critical to retinal development in this invertebrate model. The current project developed a new microfluidic system to examine the collective migration of RNBs extracted from the developing visual system of Drosophila as a model for the collective motile processes …

Fibration Symmetries Uncover The Building Blocks Of Biological Networks, Flaviano Morone, Ian Leifer, Hernán A. Makse

Publications and Research

A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these networks as a set of input trees, one for each node, which contains all pathways along which information can be transmitted in the network. In this representation, we find remarkable symmetries in the input trees that deconstruct the network into functional building blocks called fibers. Nodes in a fiber have isomorphic input trees and thus process equivalent dynamics and synchronize their activity. Each …

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 …

Accumulation Of Unacetylatable Snf2p At The Ino1 Promoter Is Detrimental To Remodeler Recycling Supply For Cup1 Induction, Michelle Esposito, Goldie Libby Sherr, Anthony Esposito, George Kaluski, Farris Ellington, Chang-Hui Shen

Publications and Research

Chromatin structure plays a decisive role in gene regulation through the actions of transcriptional activators, coactivators, and epigenetic machinery. These trans-acting factors contribute to gene expression through their interactions with chromatin structure. In yeast INO1 activation, transcriptional activators and coactivators have been defined through intense study but the mechanistic links within these trans-acting factors and their functional implications are not yet fully understood. In this study, we examined the crosstalk within transcriptional coactivators with regard to the implications of Snf2p acetylation during INO1 activation. Through various biochemical analysis, we demonstrated that both Snf2p and Ino80p chromatin remodelers accumulate …

Microfluidic Study Of The Electrocoalescence Of Aqueous Droplets In Crude Oil, Thomas Leary, Mohsen Yeganeh, Charles Maldarelli

Publications and Research

In electrocoalescence, an electric field is applied to a dispersion of conducting water droplets in a poorly conducting oil to force the droplets to merge in the direction of the field. Electrocoalescence is used in petroleum refining to separate water from crude oil and in droplet-based microfluidics to combine droplets of water in oil and to break emulsions. Using a microfluidic design to generate a two-dimensional (2D) emulsion, we demonstrate that electrocoalescence in an opaque crude oil can be visualized with optical microscopy and studied on an individual droplet basis in a chamber whose height is small enough to make …

Metabolic Reprogramming By C-Met Inhibition As A Targetable Vulnerability In Glioblastoma, Trang Thi Thu Nguyen, Enyuan Shang, Georg Karpel-Massler, Markus D. Siegelin

Publications and Research

The elucidation of better treatments for solid tumors and especially malignant glial tumors is a priority. Better understanding of the molecular underpinnings of treatment response and resistance are critical determinants in the success for this endeavor. Recently, a battery of novel tools have surfaced that allow to interrogate tumor cell metabolism to more precise extent than this was possible in the earlier days. At the forefront of these developments are the extracellular flux and carbon tracing analyses. Through utilization of these techniques our group made the recent observation that acute and chronic c-MET inhibition drives fatty acid oxidation that in …

Lamin Fofana: Blues, Alaina Claire Feldman, Dino Dincer Sirin, Lamin Fofana

Publications and Research

Catalogue for the exhibition "Lamin Fofana: Blues" presented at Baruch College's Mishkin Gallery in 2020.

Variation In Brown Rat Cranial Shape Shows Directional Selection Over 120 Years In New York City, Emily E. Puckett, Emma Sherratt, Matthew Combs, Elizabeth J. Carlen, William Harcourt-Smith, Jason Munshi-South

Publications and Research

Urbanization exposes species to novel environments and selection pressures that may change morphological traits within a population. We investigated how the shape and size of crania and mandibles changed over time within a population of brown rats (Rattus norvegicus) living in Manhattan, New York, USA, a highly urbanized environment. We measured 3D landmarks on the cranium and mandible of 62 adult individuals sampled in the 1890s and 2010s. Static allometry explained approximately 22% of shape variation in crania and mandible datasets, while time accounted for approximately 14% of variation. We did not observe significant changes in skull size through time …

Modulation Of The Pol Ii Ctd Phosphorylation Code By Rac1 And Cdc42 Small Gtpases In Cultured Human Cancer Cells And Its Implication For Developing A Synthetic-Lethal Cancer Therapy, Bo Zhang, Xuelin Zhong, Moira Sauane, Yihong Zhao, Zhi-Liang Zheng

Publications and Research

Rho GTPases, including Rho, Cdc42, Rac and ROP subfamilies, are key signaling molecules in RNA polymerase II (Pol II) transcriptional control. Our prior work has shown that plant ROP and yeast Cdc42 GTPases similarly modulate Ser2 and Ser5 phosphorylation status of the C-terminal domain (CTD) of the Pol II largest subunit by regulating CTD phosphatase degradation. Here, we present genetic and pharmacological evidence showing that Cdc42 and Rac1 GTPase signaling modulates a similar CTD Ser2 and Ser5 phosphorylation code in cultured human cancer cells. While siRNA knockdown of Cdc42 and Rac1, respectively, in HeLa cells increased the level of CTD …

Evolutionary Traits That Enable Scleractinian Corals To Survive Mass Extinction Events, Gal Dishon, Michal Grossowicz, Michael Krom, Gilad Guy, David F. Gruber, Dan Tchernov

Publications and Research

Scleractinian “stony” corals are major habitat engineers, whose skeletons form the framework for the highly diverse, yet increasingly threatened, coral reef ecosystem. Fossil coral skeletons also present a rich record that enables paleontological analysis of coral origins, tracing them back to the Triassic (~241 Myr). While numerous invertebrate lineages were eradicated at the last major mass extinction boundary, the Cretaceous-Tertiary/K-T (66 Myr), a number of Scleractinian corals survived. We review this history and assess traits correlated with K-T mass extinction survival. Disaster-related “survival” traits that emerged from our analysis are: (1) deep water residing (>100 m); (2) cosmopolitan distributions, …

Predictor Species: Improving Assessments Of Rare Species Occurrence By Modeling Environmental Co-Responses, Peter R. Thompson, William F. Fagan, Phillip P. A. Staniczenko

Publications and Research

Designing an effective conservation strategy requires understanding where rare species are located. Because rare species can be difficult to find, ecologists often identify other species called conservation surrogates that can help inform the distribution of rare species. Species distribution models typically rely on environmental data when predicting the occurrence of species, neglecting the effect of species' co-occurrences and biotic interactions. Here, we present a new approach that uses Bayesian networks to improve predictions by modeling environmental co-responses among species. For species from a European peat bog community, our approach consistently performs better than single-species models and better than conventional multi-species …

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, …

Theoretical Analysis Of The Leakage Through The Cement Line Of A Single Osteon, Gaffar Gailani, Stephen Cowin

Publications and Research

This work focuses on the Lacunar–Canalicular Porosity (PLC) of cortical bone which includes the osteons. Osteons are semicylindrical porous structures saturated with fluid within the bone and are approximately 250" role="presentation">μ" role="presentation">μm in diameter. The outer boundary of the osteon is called the cement line. Some studies suggested that the cement line is less highly mineralized and produced evidence that it has less calcium and phosphorus and more sulfur than the neighboring bone lamellae. Most authors assume that the cement line is impermeable, while others assume that some canaliculi are crossing the cement line which will make it …

Artificial Intelligence: A New Paradigm In Obstetrics And Gynecology Research And Clinical Practice, Pulwasha Iftikhar, Marcela V. Kuijpers, Azadeh Khayyat, Aqsa Iftikhar, Maribel Degouvia De Sa

Publications and Research

Artificial intelligence (AI) is growing exponentially in various fields, including medicine. This paper reviews the pertinent aspects of AI in obstetrics and gynecology (OB/GYN) and how these can be applied to improve patient outcomes and reduce the healthcare costs and workload for clinicians.

Herein, we will address current AI uses in OB/GYN, and the use of AI as a tool to interpret fetal heart rate (FHR) and cardiotocography (CTG) to aid in the detection of preterm labor, pregnancy complications, and review discrepancies in its interpretation between clinicians to reduce maternal and infant morbidity and mortality. AI systems can be used …

Proteasome Mapping Reveals Sexual Dimorphism In Tissue-Specific Sensitivity To Protein Aggregations, Edmund Charles Jenkins, Nagma Shah, Maria Gomez, Gabriella Casalena, Dazhi Zhao, Timothy C. Kenny, Sara Rose Guariglia, Giovanni Manfredi, Doris Germain

Publications and Research

Defects in the proteasome can result in pathological proteinopathies. However, the pathogenic role of sex- and tissue-specific sensitivity to proteotoxic stress remains elusive. Here, we map the proteasome activity across nine tissues, in male and female mice, and demonstrate strong sexual dimorphism in proteasome activity, where females have significantly higher activity in several tissues. Further, we report drastic differences in proteasome activity among tissues, independently of proteasome concentration, which are exacerbated under stress conditions. Sexual dimorphism in proteasome activity is confirmed in a SOD1ALS mouse model, in which the spinal cord, a tissue with comparatively low proteasome activity, is severely …

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 …

Carbon Dioxide Attracts Nesting Behavior In Captive African Naked Mole-Rats, Dan Mccloskey

Publications and Research

This dataset contains raw Radio Frequency Identification data for a 185 hour gas infusion study conducted in the TT-2 colony at the College of Staten Island in May-June 2019. The purpose of this experiment was to determine whether colony members would be attracted to a chamber with elevated carbon dioxide levels matching the highest values recorded in the typical colony nest. The results show a significant attraction to the CO2-infused chamber during and after the period of CO2 in=fusion, with the relocation of the colony nest to this site for the first time in the history of this colony. These …

Proceedings Of The Cuny Games Conference 6.0, Robert O. Duncan, Joseph Bisz, Christina Boyle, Kathleen Offenholley, Maura A. Smale, Carolyn Stallard, Deborah Sturm

Publications and Research

The CUNY Games Network is an organization dedicated to encouraging research, scholarship and teaching in the developing field of games-based learning. We connect educators from every campus and discipline at CUNY and beyond who are interested in digital and non-digital games, simulations, and other forms of interactive teaching and inquiry-based learning. These proceedings summarize the CUNY Games Conference 6.0, where scholars shared research findings at a three-day event to promote and discuss game-based pedagogy in higher education. Presenters could share findings in oral presentations, posters, demos, or play testing sessions. The conference also included workshops on how to modify existing …

Exploring Sexual Dimorphism Of The Modern Human Talus Through Geometric Morphometric Methods, Rita Sorrentino, Maria Giovanna Belcastro, Carla Figus, Nicholas B. Stephens, Kevin Turley, William Harcourt-Smith, Timothy M. Ryan, Stefano Benazzi

Publications and Research

Sex determination is a pivotal step in forensic and bioarchaeological fields.Generally,scholars focus on metric or qualitative morphological features,but in the last few years several contributions have applied geometric-morphometric (GM) techniques to overcome limitations of traditional approaches. In this study,we explore sexual dimorphism in modern human tali from three early 20th century populations (Sassari and Bologna, Italy; NewYork, USA) at intra- and interspecific population levels using geometric morphometric (GM) methods.Statistical analyses were performed using shape,form,and size variables.Our results do not show significant differences in shape between males and females, either considering the pooled sample or the individual populations. Differences in talar …

Raw Veganism: The Human Diet, Carlo Alvaro

Publications and Research

In this chapter, I present some compelling evidence that points to the conclusion that the human species has a specific diet, which is a raw vegan diet of fresh fruit, tender leafy greens, and a moderate amount of nuts and seeds. Out of the hundreds of thousands of species in the world, the only one—ours—cooks food. Not surprisingly, our species is the only one that suffers from numerous maladies. In other words, the argument is that the consumption of cooked food (especially animal-based) is unhealthful and undermines our nature. I present undeniable evidence, from evolutionary science to nutrition science, showing …

Polymers For Extrusion‐Based 3d Printing Of Pharmaceuticals: A Holistic Materials–Process Perspective, Mohammad A. Azad, Deborah Olawuni, Georgia Kimbell, Abu Zayed Badruddoza, Md. Shahadat Hossain, Tasnim Sultana

Publications and Research

Three dimensional (3D) printing as an advanced manufacturing technology is progressing to be established in the pharmaceutical industry to overcome the traditional manufacturing regime of ʹone size fits for allʹ. Using 3D printing, it is possible to design and develop complex dosage forms that can be suitable for tuning drug release. Polymers are the key materials that are necessary for 3D printing. Among all 3D printing processes, extrusion‐based (both fused deposition modeling (FDM) and pressure‐assisted microsyringe (PAM)) 3D printing is well researched for pharmaceutical manufacturing. It is important to understand which polymers are suitable for extrusion‐based 3D printing of pharmaceuticals …

The Research 101 Certificate Program At A Community College: Giving All Students The Chance To Learn Basic Information Literacy Skills, Neera Mohess

Publications and Research

Many community college students are ill prepared to do scholarly research. In order to mitigate this, librarians at our campus created the Research 101 Certificate Program in 2016. These workshops provide an access point for any student who wishes to strengthen their information literacy skill set. This essay describes the inception of the program, its pedagogical rationale, administration and participation outcomes. Suggestions for implementation at local institutions are also provided.

Exploring Innovative Ways To Incorporate The Association Of College And Research Libraries Framework In Graduate Science Teacher Education Eportfolio Projects, Alison Lehner-Quam, Wesley Pitts

Publications and Research

This article investigates ways in which student voice informed design research into information literacy instruction in a year-long graduate science education ePortfolio culminating project. Library and science education faculty partnered in a two-year project to create communities of secondary science education students, in two cohorts, who used the ACRL Framework for Information Literacy for Higher Education to support their own research and reflections into information literacy. The overarching goal was to improve the course design to help science teachers develop their professional competencies in information literacy to conduct research to support their practice. Examination of students’ responses to research experiences …