Digital Commons Network^™

Microfluidic Generated Egf-Gradients Induce Chemokinesis Of Transplantable Retinal Progenitor Cells Via The Jak/Stat And Pi3kinase Signaling Pathways, Uchenna J. Unachukwu, Moira Sauane, Maribel Vazquez, Stephen Redenti

Publications and Research

A growing number of studies are evaluating retinal progenitor cell (RPC) transplantation as an approach to repair retinal degeneration and restore visual function. To advance cell-replacement strategies for a practical retinal therapy, it is important to define the molecular and biochemical mechanisms guiding RPC motility. We have analyzed RPC expression of the epidermal growth factor receptor (EGFR) and evaluated whether exposure to epidermal growth factor (EGF) can coordinate motogenic activity in vitro. Using Boyden chamber analysis as an initial highthroughput screen, we determined that RPC motility was optimally stimulated by EGF concentrations in the range of 20-400ng/ml, with decreased stimulation …

Quantifying Reproducibility In Computational Biology: The Case Of The Tuberculosis Drugome, Daniel Garijo, Sarah Kinnings, Li Xie, Lei Xie, Yinliang Zhang, Philip E. Bourne, Yolanda Gil

Publications and Research

How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part …

Students Teaching Students: A Method For Collaborative Learning, Jean Halley, Courtney Heiserman, Victoria Felix, Amy Eshleman

Publications and Research

The Student Small Group Presentation (SSGP) model, a student-centered approach, is introduced and applied to learning communities. Similar to the jigsaw classroom, small groups of students in learning communities are responsible for teaching material to their peers. Unlike other jigsaw techniques, presentation groups in the SSGP teach an entire lesson based on collaborative work conducted outside of class. Presenters are responsible for thorough analysis of course material as they lead a discussion among a small group of peers. Students meet with the same small group throughout the semester, creating a feeling of intimate community within the larger learning community. By …

High Glucose Attenuates Shear-Induced Changes In Endothelial Hydraulic Conductivity By Degrading The Glycocalyx, Sandra V. Lopez-Quintero, Limary M. Cancel, Alexis Pierides, David Antonetti, David C. Spray, John M. Tarbell

Publications and Research

Diabetes mellitus is a risk factor for cardiovascular disease; however, the mechanisms through which diabetes impairs homeostasis of the vasculature have not been completely elucidated. The endothelium interacts with circulating blood through the surface glycocalyx layer, which serves as a mechanosensor/transducer of fluid shear forces leading to biomolecular responses. Atherosclerosis localizes typically in regions of low or disturbed shear stress, but in diabetics, the distribution is more diffuse, suggesting that there is a fundamental difference in the way cells sense shear forces. In the present study, we examined the effect of hyperglycemia on mechanotranduction in bovine aortic endothelial cells (BAEC). …

"'Jackin’ For Beats'": Djing For Citation Critique, Todd Craig

Publications and Research

A challenge in teaching English composition is helping students envision plagiarism as “borrowing” – showing love to author(s) and/or text(s) that further their argument(s), versus “stealing” – biting someone’s style and words. Alastair Pennycook (1996) and Sarah Wakefield (2006) have contributed pieces to the elaborate plagiarism/citation puzzle, while Houston Baker situated the hip-hop DJ in seminal text Black Studies, Rap and the Academy (1993). Merging these moments introduces critical questions: Did Diddy invent “the remix” or become the illest beat-biter ever? How did DJ/Producers Pete Rock and Large Professor pay homage to previous musical genres to further hip-hop remix production …

Endogenous Human Mdm2-C Is Highly Expressed In Human Cancers And Functions As A P53-Independent Growth Activator, Danielle R. Okoro, Nicoleta Arva, Chong Gao, Alla Polotskaia, Cindy Puente, Melissa Rosso, Jill Bargonetti

Publications and Research

Human cancers over-expressing mdm2, through a T to G variation at a single nucleotide polymorphism at position 309 (mdm2 SNP309), have functionally inactivated p53 that is not effectively degraded. They also have high expression of the alternatively spliced transcript, mdm2-C. Alternatively spliced mdm2 transcripts are expressed in many forms of human cancer and when they are exogenously expressed they transform human cells. However no study to date has detected endogenous MDM2 protein isoforms. Studies with exogenous expression of splice variants have been carried out with mdm2-A and mdm2-B, but the mdm2-C isoform has remained virtually unexplored. We addressed the cellular …

Linux For Academics, Part I, Steven Ovadia

Publications and Research

The article focuses on GNU/Linux, an open-source operating system based on Unix. Linux offers more choice and control to academic users. The article encourages academic users to explore Linux as a way to be more productive.

The American Association Of School Librarians (Aasl) Standards For The 21st Century Learner Lesson Plan Database, Christina Miller

Publications and Research

The American Association of School Librarians (AASL) Standards for the 21st Century Learner Lesson Plan Database (AASL Database) is a free, Open Access, interactive tool recently (2011) developed by the American Association of School Librarians, a division of the American Library Association, to assist librarians, teachers and other educators in implementing the AASL Standards for the 21st Century Learner (AASL Standards) and the Common Core State Standards. It is comprised of vetted, content-area lesson plans meant to provide excellent models to integrate AASL Standards across K-12 curricula; the platform also includes social networking features and a user portfolio. The AASL …

Womb Envy: Jean-Luc Godard's Breathless, A Woman Is A Woman, And Hail Mary, Caroline Rupprecht, Caroline Rupprecht

Publications and Research

No abstract provided.

Queer Pedagogical Desire: A Study Guide, Matt Brim

Publications and Research

This essay explores the queer pedagogical desires that attended my writing of the Study Guide for the documentary film United in Anger: A History of ACT UP (Jim Hubbard, 2012). The analysis takes up Robyn Wiegman’s central question in Object Lessons, “What is it we expect our relationship to our objects of study to do?”, which is of particular importance to the discipline of queer studies insofar as the field is oriented around the desire to meld social justice with critical pedagogy. The queer professor’s desire in the case of the Study Guide-as-object was to create a text that …

Speaking As One: Supporting Open Access With Departmental Resolutions, Madeline Cohen, Maura A. Smale, Jill Cirasella, Cynthia Tobar, Jessie Daniels

Publications and Research

Library faculty at the City University of New York (CUNY) have engaged in promoting and advocating for open access publishing at each of our campuses as well as across the University. Inspired by the passing of a faculty senate resolution in support of the creation of an open access institutional repository and associated policies, many CUNY librarians felt the need to raise their level of commitment. In this article, the authors—four library faculty members and one faculty member from outside the library—share their experiences creating and approving open access policies in the library departments of four CUNY schools and promoting …

From Tweet To Blog Post To Peer-Reviewed Article: How To Be A Scholar Now, Jessie Daniels

Publications and Research

Digital media is changing how scholars interact, collaborate, write and publish. This piece describes how to be a scholar now, when peer-reviewed articles can begin as Tweets and blog posts. In this new environment, scholars are able to create knowledge in ways that are more open, more fluid, and more easily read by wider audiences.

Β2 Adrenergic Receptor Fluorescent Protein Fusions Traffic To The Plasma Membrane And Retain Functionality, Jaclyn Bubnell, Patrick Pfister, Maria L. Sapar, Matthew E. Rogers, Paul Feinstein

Publications and Research

Green fluorescent protein (GFP) has proven useful for the study of protein interactions and dynamics for the last twenty years. A variety of new fluorescent proteins have been developed that expand the use of available excitation spectra. We have undertaken an analysis of seven of the most useful fluorescent proteins (XFPs), Cerulean (and mCerulean3), Teal, GFP, Venus, mCherry and TagRFP657, as fusions to the archetypal G-protein coupled receptor, the β2 adrenergic receptor (β2AR). We have characterized these β2AR::XFP fusions in respect to membrane trafficking and G-protein activation. We noticed that in the mouse neural cell line, OP 6, that membrane …

Lipid Metabolites Enhance Secretion Acting On Snare Microdomains And Altering The Extent And Kinetics Of Single Release Events In Bovine Adrenal Chromaffin Cells, Virginia García-Martínez, José Villanueva, Cristina J. Torregrosa-Hetland, Robert Bittman, Ashlee Higdon, Victor M. Darley-Usmar, Bazbek Davletov, Luis M. Gutiérrez

Publications and Research

Lipid molecules such as arachidonic acid (AA) and sphingolipid metabolites have been implicated in modulation of neuronal and endocrine secretion. Here we compare the effects of these lipids on secretion from cultured bovine chromaffin cells. First, we demonstrate that exogenous sphingosine and AA interact with the secretory apparatus as confirmed by FRET experiments. Examination of plasma membrane SNARE microdomains and chromaffin granule dynamics using total internal reflection fluorescent microscopy (TIRFM) suggests that sphingosine production promotes granule tethering while arachidonic acid promotes full docking. Our analysis of single granule release kinetics by amperometry demonstrated that both sphingomyelinase and AA treatments enhanced …

Students' Immersion Experiences In Study Abroad, Federica Goldoni

Publications and Research

Data show that a larger number of students than ever are participating in learning experiences abroad. However, such programs are not always as immersive and intensive as participants, faculty, program directors, and administrators would wish. This study examines the ways in which students created sustained opportunities to interact with members of the host community as well as episodes of cultural clash, miscommunication, and misunderstanding experienced at the intersection of two cultures that led to diminishing willingness to interact with members of the host community. The article concludes with recommendations for pre-departure experiences that are designed to help students become more …

Centrosomal Kinase Nek2 Cooperates With Oncogenic Pathways To Promote Metastasis, T K. Das, Dibyendu Dana, Suneeta S. Paroly, S. K. Perumal, S. Singh, H. Jhun, J. Pendse, R. L. Cagan, T. T. Talele, Sanjai Kumar

Publications and Research

Centrosomal kinase Nek2 is overexpressed in different cancers, yet how it contributes toward tumorigenesis remains poorly understood. dNek2 overexpression in a Drosophila melanogaster model led to upregulation of Drosophila Wnt ortholog wingless (Wg), and alteration of cell migration markers—Rho1, Rac1 and E-cadherin (Ecad)—resulting in changes in cell shape and tissue morphogenesis. dNek2 overexpression cooperated with receptor tyrosine kinase and mitogen-activated protein kinase signaling to upregulate activated Akt, Diap1, Mmp1 and Wg protein to promote local invasion, distant seeding and metastasis. In tumor cell injection assays, dNek2 cooperated with Ras and Src signaling to promote aggressive colonization of tumors into different …

Chimeric Rhinoviruses Displaying Mper Epitopes Elicit Anti-Hiv Neutralizing Responses, Guohua Yi, Mauro Lapelosa, Rachel Bradley, Thomas M. Mariano, Denise Elsasser Dietz, Scott Hughes, Terri Wrin, Chris Petropoulos, Emilio Gallicchio, Ronald M. Levy, Eddy Arnold, Gail Ferstandig Arnold

Publications and Research

Background: The development of an effective AIDS vaccine has been a formidable task, but remains a critical necessity. The well conserved membrane-proximal external region (MPER) of the HIV-1 gp41 glycoprotein is one of the crucial targets for AIDS vaccine development, as it has the necessary attribute of being able to elicit antibodies capable of neutralizing diverse isolates of HIV.

Methodology/Principle Findings: Guided by X-ray crystallography, molecular modeling, combinatorial chemistry, and powerful selection techniques, we designed and produced six combinatorial libraries of chimeric human rhinoviruses (HRV) displaying the MPER epitopes corresponding to mAbs 2F5, 4E10, and/or Z13e1, connected to an immunogenic …

Lizards And Lines: Selection And Demography Affect The Fate Of L1 Retrotransposons In The Genome Of The Green Anole (Anolis Carolinensis), Marc Tollis, Stéphane Boissinot

Publications and Research

Autonomous retrotransposons lacking long terminal repeats (LTR) account for much of the variation in genome size and structure among vertebrates. Mammalian genomes contain hundreds of thousands of non-LTR retrotransposon copies, mostly resulting from the amplification of a single clade known as L1. The genomes of teleost fish and squamate reptiles contain a much more diverse array of non-LTR retrotransposon families, whereas copy number is relatively low. The majority of non-LTR retrotransposon insertions in nonmammalian vertebrates also appear to be very recent, suggesting strong purifying selection limits the accumulation of non-LTR retrotransposon copies. It is however unclear whether this turnover model, …

Mood And The Market: Can Press Reports Of Investors’ Mood Predict Stock Prices?, Yochi Cohen-Charash, Charles A. Scherbaum, John D. Kammeyer-Muller, Barry M. Staw

Publications and Research

We examined whether press reports on the collective mood of investors can predict changes in stock prices. We collected data on the use of emotion words in newspaper reports on traders’ affect, coded these emotion words according to their location on an affective circumplex in terms of pleasantness and activation level, and created indices of collective mood for each trading day. Then, by using time series analyses, we examined whether these mood indices, depicting investors’ emotion on a given trading day, could predict the next day’s opening price of the stock market. The strongest findings showed that activated pleasant mood …

Bax And Bak Function As The Outer Membrane Component Of The Mitochondrial Permeability Pore In Regulating Necrotic Cell Death In Mice, Jason Karch, Jennifer Q. Kwong, Adam R. Burr, Michelle A. Sargent, John W. Elrod, Pablo M. Peixoto, Sonia Martinez-Caballero, Hanna Osinskka, Emily H-Y Cheng, Jeffrey Robbins, Kathleen W. Kinnally, Jeffrey D. Molkentin

Publications and Research

A critical event in ischemia-based cell death is the opening of the mitochondrial permeability transition pore (MPTP). However, the molecular identity of the components of the MPTP remains unknown. Here, we determined that the Bcl-2 family members Bax and Bak, which are central regulators of apoptotic cell death, are also required for mitochondrial pore-dependent necrotic cell death by facilitating outer membrane permeability of the MPTP. Loss of Bax/Bak reduced outer mitochondrial membrane permeability and conductance without altering inner membrane MPTP function, resulting in resistance to mitochondrial calcium overload and necrotic cell death. Reconstitution with mutants of Bax that cannot oligomerize …

Consumers' Perceptions Of Patient-Accessible Electronic Medical Records, Christina Zarcadoolas, Wendy L. Vaughon, Sara J. Czaja, Joslyn Levy, Maxine L. Rockoff

Publications and Research

Background: Electronic health information (eHealth) tools for patients, including patient-accessible electronic medical records (patient portals), are proliferating in health care delivery systems nationally. However, there has been very limited study of the perceived utility and functionality of portals, as well as limited assessment of these systems by vulnerable (low education level, racial/ethnic minority) consumers.

Objective: The objective of the study was to identify vulnerable consumers’ response to patient portals, their perceived utility and value, as well as their reactions to specific portal functions.

Methods: This qualitative study used 4 focus groups with 28 low education level, English-speaking consumers in June …

Patterns Of Anti-Muslim Violence In Burma: A Call For Accountability And Prevention, Andrea Gittleman, Marissa Brodney, Holly G. Atkinson

Publications and Research

In this report, the authors documents how persecution of and violence against the Rohingya in Burma has spread to other Muslim communities throughout the country. Physicians for Human Rights conducted eight separate investigations in Burma and the surrounding region between 2004 and 2013. PHR’s most recent field research in early 2013 indicates a need for renewed attention to violence against minorities and impunity for such crimes. The findings presented in this report are based on investigations conducted in Burma over two separate visits for a combined 21-day period between March and May 2013.

Β-Catenin-Independent Activation Of Tcf1/Lef1 In Human Hematopoietic Tumor Cells Through Interaction With Atf2 Transcription Factors, Luca Grumolato, Guizhong Liu, Tomomi Haremaki, Sathish Kumar Mungamuri, Phyllus Mong, Gal Akiri, Pablo Lopez-Bergami, Adriana Arita, Youssef Anouar, Marek Mlodzik, Ze'ev A. Ronai, Joshua Brody, Daniel C. Weinstein, Stuart A. Aaronson

Publications and Research

The role of Wnt signaling in embryonic development and stem cell maintenance is well established and aberrations leading to the constitutive up-regulation of this pathway are frequent in several types of human cancers. Upon ligand-mediated activation, Wnt receptors promote the stabilization of β-catenin, which translocates to the nucleus and binds to the T-cell factor/lymphoid enhancer factor (TCF/LEF) family of transcription factors to regulate the expression of Wnt target genes. When not bound to β-catenin, the TCF/LEF proteins are believed to act as transcriptional repressors. Using a specific lentiviral reporter, we identified hematopoietic tumor cells displaying constitutive TCF/LEF transcriptional activation in …

A Randomized Clinical Trial Of Trans-Dermal Nicotine Replacement In Pregnant African-American Smokers, Ayman El-Mohandes, Richard Windsor, Sylvia Tan, David C. Perry, Marie G. Gantz, Michele Kiely

Publications and Research

We compared acceptability, adherence and efficacy of trans-dermal nicotine patches and cognitive behavioral therapy (Group 1) to cognitive behavioral therapy alone (Group 2) in minority pregnant smokers. This is a randomized controlled trial. 52 women were recruited during pregnancy with a mean gestational age 18.5 ± 5.0 weeks and followed through delivery. Randomization was by site and initial cotinine levels. Interventionists and interviewers were blinded to group assignment. Two different nicotine replacement therapy dosing regiments were administered according to the baseline salivary cotinine level. A process evaluation model summarized patient adherence. The main outcome measure was self-report of cessation since …

Amanda Knox And Bella Figura, Denise Scannell Guida

Publications and Research

No abstract provided.

Scientific Communication Before And After Networked Science, John Carey

Publications and Research

Recent decades have seen extensive changes in how researchers in the sciences work. Online platforms enabled by Web 2.0 technologies (collectively known as “open” or “networked” science) have created multiple new channels for informal communications, revolutionizing the ways in which scientists collaborate and share results. Meanwhile, digitization and open access publishing have brought fundamental change to modes of publication and distribution for scientific journals. Yet the primary vehicle for the formal publication of results, the scientific article, has been much slower to alter in format. This paper will examine the functions that peer-reviewed journals have served within the scientific community …

A New Polemic: Libraries, Moocs, And The Pedagogical Landscape, Nora Almeida

Publications and Research

The Massive Open Online Course (MOOC) has emerged in the past few years as the poster child of the online higher education revolution. Lauded and derided, MOOCs (depending on who you ask) represent the democratization of education on a global scale, an overblown trend, or the beginning of the end of the traditional academic institution. MOOCs have gained so much critical traction because they have succeeded in unmooring educational exchanges and setting them adrift in the sea of the internet. Although the MOOC is a new and evolving platform, it has already upended facets of education in which librarians are …

Environmental Protection Agency Consultations With Indian Tribes: An Intercultural Struggle Over Process Of 'Consent', Denise Scannell Guida

Publications and Research

On November 6, 2000, President Bill Clinton signed his final executive order on

Consultation and Coordination with Tribal Governments. It was his last attempt to establish meaningful consultation processes with American Indians in the development of federal environmental policies. Based on ongoing environmental issues between the two cultures and the rising concern for environmental justice, the United States government wanted to identify the necessary improvements in communication and coordination among tribal and federal environmental programs, specifically regarding issues of information exchange, and creating partnerships among stakeholders. An analysis of the executive order, and a case study of the U.S. …

The Role Of Suburbia In The Attribution Of Greenhouse Gas Emissions, Jochen Albrecht, Peter Marcotullio, Andrea Sarzynski, Niels Schulz

Publications and Research

The original goal of the research presented here was to quantify by world region, the contribution of urbanized areas to global greenhouse gas (GHG) emissions (EDGAR, 2011). Regressions on population density and growth rate, GDP, and heating/cooling degree days, as well as a row of other non-significant variables, show that the contribution of urban extents is between 38% and 49% of total emissions (Marcotullio et al., 2012). In spite of using very liberal definitions of urban extents (GRUMP, 2011) this is at the low end of academic estimates (Satterthwaite, 2008; WEO, 2008; Dhakal, 2010). It is no surprise that the …

The Roles Of Sphingosine Kinase 1 And 2 In Regulating The Metabolome And Survival Of Prostate Cancer Cells, Francesca Tonelli, Manal Alossaimi, Viswanathan Natarajan, Irina Gorshkova, Evgeny Berdyshev, Robert Bittman, David G. Watson, Susan Pyne, Nigel J. Pyne

Publications and Research

We have previously shown that treatment of androgen-sensitive LNCaP cells with the sphingosine kinase (SK) inhibitor SKi (2-(p-hydroxyanilino)-4-(p-chlorophenyl)thiazole) induces the proteasomal degradation of two N-terminal variants of SK1 (SK1a and SK1b), increases C22:0-ceramide and diadenosine 5′,5′′′-P1,P3-triphosphate (Ap3A) and reduces S1P levels, and promotes apoptosis. We have now investigated the effects of three SK inhibitors (SKi, (S)-FTY720 vinylphosphonate, and (R)-FTY720 methyl ether) on metabolite and sphingolipid levels in androgen-sensitive LNCaP and androgen-independent LNCaP-AI prostate cancer cells. The 51 kDa N-terminal variant of SK1 (SK1b) evades the proteasome in LNCaP-AI cells, and these cells do not exhibit an increase in C22:0-ceramide or …