Digital Commons Network^™

Identifying And Analyzing Rna Pseudoknots Based On Graph-Theoretical Properties Of Dual Graphs: A Partitioning Approach, Louis Petingi

Publications and Research

In this paper we propose the study of properties of RNA secondary structures modeled as dual graphs, by partitioning these graphs into topological components denominated blocks. We give a full characterization of possible topological configurations of these blocks, and, in particular we show that an RNA secondary structure contains a pseudoknot if and only if its corresponding dual graph contains a block having a vertex of degree at least 3. Once a dual graph has been partitioned via computationally-efficient well-known graph-theoretical algorithms, this characterization allow us to identify these sub-topologies and physically isolate pseudoknots from RNA secondary structures and analyze …

Microbial Stimulation And Succession Following A Test Well Injection Simulating Co₂ Leakage Into A Shallow Newark Basin Aquifer, Gregory O'Mullan, M. Elias Dueker, Kale Clauson, Qiang Yang, Kelsey Umemoto, Natalia Zakharova, Juerg Matter, Martin Stute, Taro Takahashi, David Goldberg

Publications and Research

In addition to efforts aimed at reducing anthropogenic production of greenhouse gases, geological storage of CO2 is being explored as a strategy to reduce atmospheric greenhouse gas emission and mitigate climate change. Previous studies of the deep subsurface in North America have not fully considered the potential negative effects of CO2 leakage into shallow drinking water aquifers, especially from a microbiological perspective. A test well in the Newark Rift Basin was utilized in two field experiments to investigate patterns of microbial succession following injection of CO2-saturated water into an isolated aquifer interval, simulating a CO2 leakage scenario. A decrease in …

Synthesis Of Dinucleoside Acylphosphonites By Phosphonodiamidite Chemistry And Investigation Of Phosphorus Epimerization, William H. Hersh

Publications and Research

The reaction of the diamidite, (iPr2N)2PH, with acyl chlorides proceeds with the loss of HCl to give the corresponding acyl diamidites, RC(O)P(N(iPr)2)2 (R = Me (7), Ph (9)), without the intervention of sodium to give a phosphorus anion. The structure of 9 was confirmed by single-crystal X-ray diffraction. The coupling of the diamidites 7 and 9 with 5′-O-DMTr-thymidine was carried out with N-methylimidazolium triflate as the activator to give the monoamidites 3′-O-(P(N(iPr)2)C(O)R)-5′-O-DMTr-thymidine, and further coupling with 3′-O-(tert-butyldimethylsilyl)thymidine was carried out with activation by pyridinium trifluoroacetate/Nmethylimidazole. The new dinucleoside acylphosphonites could be further oxidized, hydrolyzed to the H-phosphonates, and sulfurized to …

A Quantitative Analysis Of The Relationship Between An Online Homework System And Student Achievement In Pre-Calculus, Parisa Babaali, Lidia Gonzalez

Publications and Research

Supporting student success in entry-level mathematics courses at the undergraduate level has and continues to be a challenge. Recently we have seen an increased reliance on technological supports including software to supplement more traditional in-class instruction. In this paper, we explore the effects on student performance of the use of a computer software program to supplement instruction in an entry-level mathematics course at the undergraduate level, specifically, a pre-calculus course. Relying on data from multiple sections of the course over various semesters, we compare student performance in those classes utilizing the software against those in which it was not used. …

Theories In Spin Dynamics Of Solid-State Nuclear Magnetic Resonance Spectroscopy, Eugene S. Mananga, Jalil Moghaddasi, Ajaz Sana, Mostafa Sadoqi

Publications and Research

This short review article presents theories used in solid-state nuclear magnetic resonance spectroscopy. Main theories used in NMR include the average Hamiltonian theory, the Floquet theory and the developing theories are the Fer expansion or the Floquet-Magnus expansion. These approaches provide solutions to the time-dependent Schrodinger equation which is a central problem in quantum physics in general and solid-state nuclear magnetic resonance in particular. Methods of these expansion schemes used as numerical integrators for solving the time dependent Schrodinger equation are presented. The action of their propagator operators is also presented. We highlight potential future theoretical and numerical directions such …

A Recipe For The Estimation Of Information Flow In A Dynamical System, Deniz Gencaga, Kevin H. Knuth, William B. Rossow

Publications and Research

Information-theoretic quantities, such as entropy and mutual information (MI), can be used to quantify the amount of information needed to describe a dataset or the information shared between two datasets. In the case of a dynamical system, the behavior of the relevant variables can be tightly coupled, such that information about one variable at a given instance in time may provide information about other variables at later instances in time. This is often viewed as a flow of information, and tracking such a flow can reveal relationships among the system variables. Since the MI is a symmetric quantity; an asymmetric …

Variation In Rheumatoid Hand And Wrist Surgery Among Medicare Beneficiaries: A Population-Based Cohort Study, Lin Zhong, Kevin C. Chung, Onur Baser, David A. Fox, Huseyin Yuce, Jennifer F. Waljee

Publications and Research

Objective. To examine the rate and variation in rheumatoid arthritis (RA)-related hand and wrist surgery among Medicare (elderly) beneficiaries in the United States, and to identify the patient and provider factors that influence surgical rates.

Methods. Using the 2006–2010 100% Medicare claims data of beneficiaries with RA diagnosis, we examined rates of rheumatoid hand and wrist arthroplasty, arthrodesis, and hand tendon reconstruction in the United States. We used multivariate logistic regression models to examine variation in receipt of surgery by patient and regional characteristics (density of providers, intensity of use of biologic disease-modifying antirheumatic drugs).

Results. Between 2006 and 2010, …

A Replication Of Failure, Not A Failure To Replicate, Gary Holden, Kathleen Barker, Sofie Kuppens, Gary Rosenberg, Jonathan`

Publications and Research

Purpose: The increasing role of systematic reviews in knowledge production demands greater rigor in the literature search process. The performance of the Social Work Abstracts (SWA) database has been examined multiple times over the past three decades. The current study is a replication within this line of research.

Method: Issue level coverage was examined for the same 33 SWA core journals and the same time period as our 2009 study.

Results: The mean percentage of issues missing in the current study was 20%. The mean percentage of issues missing in the current study was significantly greater than …

Configurationally Stable, Enantioenriched Organometallic Nucleophiles In Stereospecific Pd-Catalyzed Cross-Coupling Reactions: An Alternative Approach To Asymmetric Synthesis, Chao-Yuan Wang, Joseph Derosa, Mark R. Biscoe

Publications and Research

Several research groups have recently developed methods to employ configurationally stable, enantioenriched organometallic nucleophiles in stereospecific Pd-catalyzed cross-coupling reactions. By establishing the absolute configuration of a chiral alkyltin or alkylboron nucleophile prior to its use in cross-coupling reactions, new stereogenic centers may be rapidly and reliably generated with preservation of the known initial stereochemistry. While this area of research is still in its infancy, such stereospecific cross-coupling reactions may emerge as simple, general methods to access diverse, optically active products from common enantioenriched organometallic building blocks. This minireview highlights recent progress towards the development of general, stereospecific Pd-catalyzed crosscoupling reactions …

U.S. Needs To Increase Its Scientific Literacy, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Stereoselective Radical C–H Alkylation With Acceptor/Acceptor-Substituted Diazo Reagents Via Co(Ii)-Based Metalloradical Catalysis, Xin Cui, Xue Xu, Li-Men Jin, Lukasz Wojtas, X. Peter Zhang

Publications and Research

Co(II)-based metalloradical catalysis has, for the first time, been successfully applied for asymmetric intramolecular C–H alkylation of acceptor/acceptor-substituted diazo reagents. Through the design and synthesis of a new D₂-symmetric chiral amidoporphyrin as the supporting ligand, the Co(II)-based metalloradical system, which operates at room temperature, is capable of 1,5-C–H alkylation of α-methoxycarbonyl-α-diazosulfones with a broad range of electronic properties, providing the 5-membered sulfolane derivatives in high yields with excellent diastereoselectivities and enantioselectivities. In addition to complete chemoselectivity toward allylic and allenic C–H bonds, the Co(II)-based metalloradical catalysis for asymmetric C–H alkylation features a remarkable degree of functional group tolerance.

Women, Minorities Face Prejudice In Academia, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Claims Of Demise Of Humanities Greatly Exaggerated, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Considerations Are Many When Choosing A Major, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Examination Of Geophysical Signatures Of Ethanol-Water Mixtures In A Homogeneous Sand Column Using Ground Penetrating Radar And Time-Domain Reflectometry, Angelo Lampousis, Neil Terry, Lee Slater

Publications and Research

In recent years there has been an increase in the frequency of incidents involving ethanol-blended gasoline affecting the groundwater. Near-surface geophysical methods hold promise for site characterization at ethanol contaminated sites. We attempted to record the broadband dielectric properties of ethanol at various concentrations as it was circulating through a closed tank containing either sand or a sand-clay mixture. Two high frequency GPR antennas were positioned symmetrically on either side of the sample holder to obtain transmission measurements. In the first part of the experiment we used a sample consisting of sand. In the second part of the experiment we …

Can Group Discussions And Individualized Assignments Help More Students Succeed In Developmental Mathematics?, Reem Jaafar

Publications and Research

Students taking developmental mathematics courses resist attempting word problems when they are presented to them. Although word problems can help students contextualize learning, develop better understanding of the concepts and apply world knowledge, they constitute an impediment to students’ progress in developmental mathematics courses. A two-semester study on the first developmental mathematics course at LaGuardia Community College shows that students perform better at word problems when they have been discussed in groups with their peers prior to the homework. Moreover, when assigned word problems without a class discussion, students perform better when these problems are individualized based on their areas …

Curriculum Integration: The Experience Of Three Founding Faculty At A New Community College, Nicole Saint-Louis, Karla Fuller, Naveen Seth

Publications and Research

This article explores the design and implementation of the curriculum for City Seminar, an integrated course in the first-year experience at a new community college. This interdisciplinary course focuses on a critical issue that provides content and context for quantitative reasoning (QR), reading, and writing (RW) to strengthen students’ developmental skills. This integrated curriculum is taught in a learning community. Its goals include greater information retention, better transfer of knowledge and developmental skills-building while students earn college credit. These tie in with the College’s overarching goals of improving retention and graduation rates. Early results from this curriculum are encouraging.

Google Vs. The Library (Part Iii): Assessing The Quality Of Sources Found By Undergraduates, Helen Georgas

Publications and Research

This study assesses and compares the quality of sources found by undergraduate students when doing research using both Google and a library (federated) search tool. Thirty undergraduates were asked to find four sources (one book, two articles, and one additional source of their choosing) related to a selected research topic. Students used both Google and a federated search (resource discovery) tool to find material they believed to be relevant. Each source was evaluated for topic relevance, authority, appropriateness, and date, and assigned a total quality score. Results showed that the books found via Google were slightly higher quality than those …

Connecting Science Education To A World In Crisis, Kenneth Tobin

Publications and Research

Even though humanity faces grand challenges, including climate change, sustainability of the planet and its resources, and well-being of humans and other species, for the past 60 years science educators have been preoccupied with much the same priorities. Adherence to the tenets of crypto-positivism creates problems for research in the social sciences (e.g., over reliance on statistical analyses leads to oversimplified models that strip away context and are reductive). Hypotheses and associated statistical tests support causal models that rarely predict social conduct or blaze pathways for meaningful transformation. In contrast to the mainstream of research in science education, I advocate …

Global Trends In Extreme Precipitation: Climate Models Versus Observations, Behzad Asadieh, Nir Y. Krakauer

Publications and Research

Precipitation events are expected to become substantially more intense under global warming, but few global comparisons of observations and climate model simulations are available to constrain predictions of future changes in precipitation extremes. We present a systematic global-scale comparison of changes in historical (1901–2010) annual-maximum daily precipitation between station observations (compiled in HadEX2) and the suite of global climate models contributing to the fifth phase of the Coupled Model Intercomparison Project (CMIP5). We use both parametric and non-parametric methods to quantify the strength of trends in extreme precipitation in observations and models, taking care to sample them spatially and temporally …

Early Detection And Monitoring Of Malaria, Md Zahidur Rahman, Leonid Roytman, Abdelhamid Kadik, Howard Miller, Dilara A. Rosy

Publications and Research

Global Earth Observation Systems of Systems (GEOSS) are bringing vital societal benefits to people around the globe. In this research article, we engage undergraduate students in the exciting area of space exploration to improve the health of millions of people globally. The goal of the proposed research is to place students in a learning environment where they will develop their problem solving skills in the context of a world crisis (e.g., malaria). Malaria remains one of the greatest threats to public health, particularly in developing countries. The World Health Organization has estimated that over one million die of Malaria each …

Toxins In Newtown Creek, Burl Yearwood, Cho Cho Aung, Ridima Pradhan, Jennifer Vance

Publications and Research

Newtown Creek is a 3.5 mile river which empties into the East River in New York, United States. The river runs the boundary between the Queens and Brooklyn Burroughs. A thriving sight of industry, this river has been the location of much pollution for over a century. Battered by oil spills and oil seepage, raw sewage, trash carried by rain water, cement, animal fat, and a 15 meter sludge on the bottom of the riverbed, Newtown Creek is one of the most polluted waterways in the United States. In this article, data for nitrate, phosphate, lead, copper, dissolved iron, and …

Using Diagrams Versus Text For Spaced Restudy: Effects On Learning In 10th Grade Biology Classes, Bradley W. Bergey, Jennifer G. Cromley, Amanda Kirchgessner, Nora S. Newcombe

Publications and Research

BackgroundandAim. Spacedrestudyhasbeentypicallytestedwithwrittenlearning materials, but restudy with visual representations in actual classrooms is under- researched. We compared the effects of two spaced restudy interventions: A Diagram- Based Restudy (DBR) warm-up condition and a business-as-usual Text-Based Restudy (TBR) warm-up condition.

Sample. One hundred and twenty-eight consented high school students in 15 classes.

Methods. Students completed daily warm-ups over a 4-week period. Students were randomly assigned to conditions within classrooms. Warm-ups were independently completed at the start of class meetings and consisted of questions about content covered 1–10 days prior to each warm-up. Students received feedback on their answers each week. A series …

Teaching High School Biology Students To Coordinate Text And Diagrams: Relations With Transfer, Effort, And Spatial Skill, Bradley W. Bergey, Jennifer G. Cromley, Nora S. Newcombe

Publications and Research

There is growing evidence that targeted instruction can improve diagram comprehension, yet one of the skills identified in the diagram comprehension literature—coordinating multiple representations —has rarely been directly taught to students and tested as a classroom intervention. We created a Coordinating Multiple Representation (CMR) intervention that was an addition to an intervention focused on Conventions of Diagrams (COD) and tested their joint effects on diagram comprehension for near transfer (uninstructed biology diagrams), far transfer (uninstructed geology diagrams), and content learning (biology knowledge). The comparison group received instruction using a previously validated intervention that focused exclusively on COD. Participants were 9th–10th …

Numeracy Infusion Course For Higher Education (Niche), 1: Teaching Faculty How To Improve Students' Quantitative Reasoning Skills Through Cognitive Illusions, Frank Wang, Esther I. Wilder

Publications and Research

We describe one of the eight units of a professional development program, the Numeracy Infusion Course for Higher Education (NICHE), which introduces research on cognition, including dual-processing theories, to university faculty. Under the dual-processing framework, System 1 (intuition) quickly proposes intuitive answers to judgment problems as they arise, while System 2 (deliberation) monitors the quality of these proposals, which it may endorse, correct, or override. We present several classic questions that demonstrate the pitfalls of overreliance on intuition without analytical thinking, then describe faculty participants’ responses to these questions and their ideas on how to apply cognitive illusion research to …

Liquidity Premiums In A Levy Market, Mei Xing

Publications and Research

This paper gives a theorem for the continuous time super-replication cost of European options where the stock price follows an exponential Levy process. Under a mild assumption on the legend transform of the trading cost function, the limit of the sequence of the discrete super-replication cost is proved to be greater than or equal to an optimal control problem. The main tool is an approximation multinomial scheme based on a discrete grid on a finite time interval [0,1] for a pure jump Levy model. This multinomial model is constructed similar to that proposed by (Szimayer & Maller, Stoch. Proce. & …

The Case Of The Disappearing E-Book: Academic Libraries And Subscription Packages, Helen Georgas

Publications and Research

One of the standard models for e-book licensing in academic libraries is the subscription package. This study is a one-year analysis of "disappeared" titles from ebrary's Academic Complete™ collection. During 2013, 3462 titles were deleted. Deleted titles were mainly recent publications (published within the last ten years), with a high number of deletions within the broad subject areas of the social sciences (H), language and literature (P), and history (C, D, E, F). Deleted titles were evenly divided between monographs published by popular presses, and monographs published by scholarly or university presses. It is recommended that deleted titles be closely …

Wetchimp-Wsl: Intercomparison Of Wetland Methane Emissions Models Over West Siberia, T. J. Bohn, J. R. Melton, A. Ito, T. Kleinen, R. Spahni, B. D. Stocker, B. Zhang, X. Zhu, R. Schroeder, M. V. Glagolev, S. Maksyutov, V. Brovkin, G. Chen, S. N. Denisov, A. V. Eliseev, A. Gallego-Sala, K. C. Mcdonald, M. A. Rawlins, W. J. Riley, Z. M. Subin, H. Tian, Q. Zhuang, J. O. Kaplan

Publications and Research

Wetlands are the world’s largest natural source of methane, a powerful greenhouse gas. The strong sensitivity of methane emissions to environmental factors such as soil temperature and moisture has led to concerns about potential positive feedbacks to climate change. This risk is particularly relevant at high latitudes, which have experienced pronounced warming and where thawing permafrost could potentially liberate large amounts of labile carbon over the next 100 years. However, global models disagree as to the magnitude and spatial distribution of emissions, due to uncertainties in wetland area and emissions per unit area and a scarcity of in situ observations. …

Capstone Interdisciplinary Team Project: A Requirement For The Ms In Sustainability Degree, Latif M. Jiji, Irvin Sam Schonfeld, George A. Smith

Publications and Research

Purpose – This paper aims to describe experience gained with a required six-credit year-long course, the Capstone Interdisciplinary Team Project, a key component of the Master of Science (MS) in Sustainability degree at the City College of New York. A common feature of sustainability problems is their interdisciplinary nature. Solutions to sustainability problems often require professionals with different training and backgrounds to work as a team. A sustainability curriculum should provide students with the skills needed to competently participate in an interdisciplinary team.

Design/methodology/approach – Instructors drawn from different departments and divisions of the college developed a pool of sustainability-focused …

Developing Moocs To Narrow The College Readiness Gap: Challenges And Recommendations For A Writing Course, Shoba Bandi-Rao, Christopher Devers

Publications and Research

Massive Open Online Courses (MOOCs) have demonstrated the potential to deliver quality and cost effective course materials to large numbers of students. Approximately 60% of first-year students at community colleges are underprepared for college-level coursework. One reason for low graduation rates is the lack of the overall college readiness. MOOCs offering "remedial" writing have the potential to better prepare high school graduates for college, thereby increasing their chances of completing a degree and reducing the cost of education for students, families, institutions, and taxpayers. However, MOOCs are typically more suitable for motivated and prepared students. Designing a MOOC on writing …