Digital Commons Network^™

Peak Electric Load Relief In Northern Manhattan: An Exploratory Data Analysis, Hildegaard D. Link, José Pillich, Yehuda L. Klein

Publications and Research

The aphorism “Think globally, act locally,” attributed to René Dubos, reflects the vision that the solution to global environmental problems must begin with efforts within our communities. PlaNYC 2030, the New York City sustainability plan, is the starting point for this study. Results include (a) a case study based on the City College of New York (CCNY) energy audit, in which we model the impacts of green roofs on campus energy demand and (b) a case study of energy use at the neighborhood scale. We find that reducing the urban heat island effect can reduce building cooling requirements, peak electricity …

Facile Synthesis Of 1-Alkoxy-1h-Benzo- And 7-Azabenzotriazoles From Peptide Coupling Agents, Mechanistic Studies, And Synthetic Applications, Mahesh K. Lakshman, Manish K. Singh, Mukesh Kumar, Raghu Ram Chamala, Vijayender R. Yedulla, Domenick Wagner, Evan Leung, Lijia Yang, Asha Matin, Sadia Ahmad

Publications and Research

(1H-Benzo[d][1,2,3]triazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP), 1H-benzo[d][1,2,3]triazol-1-yl 4-methylbenzenesulfonate (Bt-OTs), and 3H-[1,2,3]triazolo[4,5-b]pyridine-3-yl 4-methylbenzenesulfonate (At-OTs) are classically utilized in peptide synthesis for amide-bond formation. However, a previously undescribed reaction of these compounds with alcohols in the presence of a base, leads to 1-alkoxy-1H-benzo- (Bt-OR) and 7-azabenzotriazoles (At-OR). Although BOP undergoes reactions with alcohols to furnish 1-alkoxy-1H-benzotriazoles, Bt-OTs proved to be superior. Both, primary and secondary alcohols undergo reaction under generally mild reaction conditions. Correspondingly, 1-alkoxy-1H-7-azabenzotriazoles were synthesized from At-OTs. Mechanistically, there are three pathways by which these peptide-coupling agents can react with alcohols. From 31P{1H}, [18O]-labeling, and other chemical experiments, phosphonium and tosylate derivatives of …

Systems Biology Of Cancer: A Challenging Expedition For Clinical And Quantitative Biologists, Ilya Korsunsky, Kathleen Mcgovern, Tom Lagatta, Loes Olde Loohuis, Terri Grosso-Applewhite, Nancy Griffeth, Bud Mishra

Publications and Research

A systems-biology approach to complex disease (such as cancer) is now complementing traditional experience-based approaches, which have typically been invasive and expensive. The rapid progress in biomedical knowledge is enabling the targeting of disease with therapies that are precise, proactive, preventive, and personalized. In this paper, we summarize and classify models of systems biology and model checking tools, which have been used to great success in computational biology and related fields. We demonstrate how these models and tools have been used to study some of the twelve biochemical pathways implicated in but not unique to pancreatic cancer, and conclude that …

Rejection Positivity Predicts Trial-To-Trial Reaction Times In An Auditory Selective Attention Task: A Computational Analysis Of Inhibitory Control, Sufen Chen, Robert D. Melara

Publications and Research

A series of computer simulations using variants of a formal model of attention (Melara and Algom, 2003) probed the role of rejection positivity (RP), a slow-wave electroencephalographic (EEG) component, in the inhibitory control of distraction. Behavioral and EEG data were recorded as participants performed auditory selective attention tasks. Simulations that modulated processes of distractor inhibition accounted well for reaction-time (RT) performance, whereas those that modulated target excitation did not. A model that incorporated RP from actual EEG recordings in estimating distractor inhibition was superior in predicting changes in RT as a function of distractor salience across conditions. A …

Rejection Positivity Predicts Trial-To-Trial Reaction Times In An Auditory Selective Attention Task: A Computational Analysis Of Inhibitory Control, Sufen Chen, Robert D. Melara

Publications and Research

A series of computer simulations using variants of a formal model of attention (Melara and Algom, 2003) probed the role of rejection positivity (RP), a slow-wave electroencephalographic (EEG) component, in the inhibitory control of distraction. Behavioral and EEG data were recorded as participants performed auditory selective attention tasks. Simulations that modulated processes of distractor inhibition accounted well for reaction-time (RT) performance, whereas those that modulated target excitation did not. A model that incorporated RP from actual EEG recordings in estimating distractor inhibition was superior in predicting changes in RT as a function of distractor salience across conditions. A model that …

Gosam-2.0: A Tool For Automated One-Loop Calculations Within Thestandard Model And Beyond, Gavin Cullen, Hans Van Deurzen, Nicolas Greiner, Gudrun Heinrich, Gionata Luisoni, Pierpaolo Mastrolia, Edoardo Mirabella, Giovanni Ossola, Tiziano Peraro, Johannes Schlenk, Johann Felix Von Soden-Fraunhofen, Francesco Tramontano

Publications and Research

We present the version 2.0 of the program pack-ageGoSamfor the automated calculation of one-loop ampli-tudes.GoSamis devised to compute one-loop QCD and/orelectroweak corrections to multi-particle processes withinand beyond the Standard Model. The new code containsimprovements in the generation and in the reduction of theamplitudes, performs better in computing time and numer-ical accuracy, and has an extended range of applicability.The extended version of the “Binoth-Les-Houches-Accord”interface to Monte Carlo programs is also implemented. Wegive a detailed description of installation and usage of thecode, and illustrate the new features in dedicated examples.

Wigner High-Electron-Correlation Regime Of Nonuniform Density Systems: A Quantal-Density-Functional-Theory Study, Douglas Achan, Lou Massa, Viraht Sahni

Publications and Research

The Wigner regime of a system of electrons in an external field is characterized by a low electron density and a high electron-interaction energy relative to the kinetic energy. The low-correlation regime is in turn described by a high electron density and an electron-interaction energy smaller than the kinetic energy. The Wigner regime of a nonuniform-electron-density system is investigated via quantal density functional theory (QDFT). Within QDFT, the contributions of electron correlations due to the Pauli exclusion principle, Coulomb repulsion, and correlation-kinetic effects are separately delineated and explicitly defined. The nonuniform-electron-density system studied is that of the Hooke's atom in …

Carbon Partitioning In Green Algae (Chlorophyta) And The Enolase Enzyme, Jürgen E. W. Polle, Peter Neofotis, Andy Huang, William Chang, Kiran Sury, Eliza M. Wiech

Publications and Research

The exact mechanisms underlying the distribution of fixed carbon within photoautotrophic cells, also referred to as carbon partitioning, and the subcellular localization of many enzymes involved in carbon metabolism are still unknown. In contrast to the majority of investigated green algae, higher plants have multiple isoforms of the glycolytic enolase enzyme, which are differentially regulated in higher plants. Here we report on the number of gene copies coding for the enolase in several genomes of species spanning the major classes of green algae. Our genomic analysis of several green algae revealed the presence of only one gene coding for a …

Audience Preferences Are Predicted By Temporal Reliability Of Neural Processing, Jacek P. Dmochowski, Matthew A. Bezdek, Brian P. Abelson, John S. Johnson, Eric H. Schumacher, Lucas C. Parra

Publications and Research

Naturalistic stimuli evoke highly reliable brain activity across viewers. Here we record neural activity from a group of naive individuals while viewing popular, previously-broadcast television content for which the broad audience response is characterized by social media activity and audience ratings. We find that the level of inter-subject correlation in the evoked encephalographic responses predicts the expressions of interest and preference among thousands. Surprisingly, ratings of the larger audience are predicted with greater accuracy than those of the individuals from whom the neural data is obtained. An additional functional magnetic resonance imaging study employing a separate sample of subjects shows …

Differential Basolateral–Apical Distribution Of Scavenger Receptor, Class B, Type I In Cultured Cells And The Liver, Stefanie Fruhwürth, Werner J. Kovacs, Robert Bittman, Simon Messner, Clemens Röhrl, Herbert Stangl

Publications and Research

The high-density lipoprotein (HDL) receptor, scavenger receptor class B, type I (SR-BI), mediates selective cholesteryl ester uptake into the liver, which finally results in cholesterol secretion into the bile. Despite several reports, the distribution of hepatic SR-BI between the sinusoidal and canalicular membranes is still under debate. We present immunohistological data using specific markers showing that the bulk of SR-BI is present in sinusoidal membranes and, to a lesser extent, in canalicular membranes in murine and human liver sections. In addition, SR-BI was detected in preparations of rat liver canalicular membranes. We also compared the in vivo findings to HepG2 …

Comorbidity Of Infectious Diseases And Anxiety Disorders In Adults And Its Association With Quality Of Life: A Community Study, Cornelia Witthauer, Andrew T. Gloster, Andrea Hans Meyer, Renee D. Goodwin, Roselind Lieb

Publications and Research

Objective: Infectious diseases and anxiety disorders are common and both are associated with substantial burden to individual, families, and society. A better understanding of their association may be helpful in explicating possible etiological mechanisms related to both. The goal of the current study was to investigate the relationship between specific infectious diseases and anxiety disorders among adults in the community, and to examine whether the co-occurrence of the two is associated with poorer quality of life compared to subjects with one or neither condition.

Methods: We used data from the 1998 German Mental Health survey with 4181 subjects aged 18–65. …

Structural Differentiation Of Graphs Using Hosoya-Based Indices, Matthias Dehmer, Abbe Mowshowitz, Yongtang Shi

Publications and Research

In this paper, we introduce the Hosoya-Spectral indices and the Hosoya information content of a graph. The first measure combines structural information captured by partial Hosoya polynomials and graph spectra. The latter is a graph entropy measure which is based on blocks consisting of vertices with the same partial Hosoya polynomial. We evaluate the discrimination power of these quantities by interpreting numerical results.

A Good Compromise: Rapid And Robust Species Proxies For Inventorying Biodiversity Hotspots Using The Terebridae (Gastropoda: Conoidea), Maria Vittoria Modica, Nicolas Puillandre, Magalie Castelin, Yu Zhang, Mandë Holford

Publications and Research

Devising a reproducible approach for species delimitation of hyperdiverse groups is an ongoing challenge in evolutionary biology. Speciation processes combine modes of passive and adaptive trait divergence requiring an integrative taxonomy approach to accurately generate robust species hypotheses. However, in light of the rapid decline of diversity on Earth, complete integrative approaches may not be practical in certain species-rich environments. As an alternative, we applied a two-step strategy combining ABGD (Automated Barcode Gap Discovery) and Klee diagrams, to balance speed and accuracy in producing primary species hypotheses (PSHs). Specifically, an ABGD/Klee approach was used for species delimitation in the Terebridae, …

Decolorization Of Hair Dye By Lignocellulosic Waste Materials From Contaminated Waters, Habib Zahir, Michelle Naidoo, Rada-Mayya Kostadinova, Karla A. Ortiz, Rosario Sun-Kuo, Abel E. Navarro

Publications and Research

Basic yellow 57 (BY57) was chosen as a model hair dye due to its prevalence in cosmetics wastewaters. This study proposes the use of lignocellulosic materials like spent tea leaves of peppermint (PM), chai tea (CT), and chamomile (CM) as raw adsorbents for the removal of BY57 from contaminated solutions. Batch adsorption experiments were carried out at room temperature to achieve the maximum adsorption capacity. Results indicate that the highest removal is achieved at pH 6–8, with a minimum adsorbent mass of 75 mg and in the absence of salinity, crowding agents and heavy metals. Adsorption equilibria were modeled according …

Evaluation Of A New Method Of Fossil Retrodeformation By Algorithmic Symmetrization: Crania Of Papionins (Primates, Cercopithecidae) As A Test Case, Melissa Tallman, Nina Amenta, Eric Delson, Stephen R. Frost, Deboshmita Ghosh, Zachary S. Klukkert, Andrea Morrow, Gary J. Sawyer

Publications and Research

Diagenetic distortion can be a major obstacle to collecting quantitative shape data on paleontological specimens, especially for three-dimensional geometric morphometric analysis. Here we utilize the recently -published algorithmic symmetrization method of fossil reconstruction and compare it to the more traditional reflection & averaging approach. In order to have an objective test of this method, five casts of a female cranium of Papio hamadryas kindae were manually deformed while the plaster hardened. These were subsequently “retrodeformed” using both algorithmic symmetrization and reflection & averaging and then compared to the original, undeformed specimen. We found that in all cases, algorithmic retrodeformation improved …

Modeling And Analysis Of Neural Spike Trains, Wei Wu, Asohan Amarasingham, Zhe (Sage) Chen, Sung-Phil Kim

Publications and Research

No abstract provided.

Searching For Superspreaders Of Information In Real-World Social Media, Sen Pei, Lev Muchnik, José S. Andrade, Jr., Zhiming Zheng, Hernán A. Makse

Publications and Research

A number of predictors have been suggested to detect the most influential spreaders of information in online social media across various domains such as Twitter or Facebook. In particular, degree, PageRank, k-core and other centralities have been adopted to rank the spreading capability of users in information dissemination media. So far, validation of the proposed predictors has been done by simulating the spreading dynamics rather than following real information flow in social networks. Consequently, only model-dependent contradictory results have been achieved so far for the best predictor. Here, we address this issue directly. We search for influential spreaders by following …

On The Effects Of Competition Between Agent-Based Double Auction Markets, Kai Cai, Jinzhong Niu, Simon Parsons

Publications and Research

Real market institutions, stock and commodity exchanges for example, do not occur in isolation. The same stocks and commodities may be listed on multiple exchanges, and traders who want to deal in those goods have a choice of markets in which to trade. While there has been extensive research into agent-based trading in individual markets, there is little work on this kind of multiple market scenario. Our work seeks to address this imbalance, examining how standard economic measures, like allocative efficiency, are affected by the presence of multiple markets for the same good. We find that while dividing traders between …

Case Study: From Gummy Bears To Celery Stalks: Diffusion And Osmosis, Kevin M. Bonney

Publications and Research

The article describes a case study which interperses information on diffusion and osmosis with content review and knowledge application questions, as well as simple experiment that can be conducted without the use of a laboratory. Topics discussed include biological membranes, the use of gummy bears to demonstrate osmosis and osmosis in animal cells. Also mentioned is osmosis in plants. It notes that the case study was developed for use in an introductory undergraduate biology course.

The Create Strategy For Intensive Analysis Of Primary Literature Can Be Used Effectively By Newly Trained Faculty To Produce Multiple Gains In Diverse Students, Leslie M. Stevens, Sally G. Hoskins

Publications and Research

The CREATE (Consider Read, Elucidate the hypotheses, Analyze and interpret the data, and Think of the next Experiment) strategy aims to demystify scientific research and scientists while building critical thinking, reading/analytical skills, and improved science attitudes through intensive analysis of primary literature. CREATE was developed and piloted at the City College of New York (CCNY), a 4-yr, minority-serving institution, with both upper-level biology majors and first-year students interested in science, technology, engineering, and mathematics. To test the extent to which CREATE strategies are broadly applicable to students at private, public, research-intensive, and/or primarily undergraduate colleges/universities, we trained a cohort of …

Looking For Cosmic Neutrino Background, Chiaki Yanagisawa

Publications and Research

Since the discovery of neutrino oscillation in atmospheric neutrinos by the Super-Kamiokande experiment in 1998, study of neutrinos has been one of exciting fields in high-energy physics. All the mixing angles were measured. Quests for (1) measurements of the remaining parameters, the lightest neutrino mass, the CP violating phase(s), and the sign of mass splitting between the mass eigenstates m₃ and m₁, and (2) better measurements to determine whether the mixing angle θ₂₃ is less than π/4, are in progress in a well-controlled manner. Determining the nature of neutrinos, whether they are Dirac or Majorana particles …

Environmental Data Analysis And Remote Sensing For Early Detection Of Dengue And Malaria, Md Zahidur Rahman, Leonid Roytman, Abdelhamid Kadik, Dilara A. Rosy

Publications and Research

Malaria and dengue fever are the two most common mosquito-transmitted diseases, leading to millions of serious illnesses and deaths each year. Because the mosquito vectors are sensitive to environmental conditions such as temperature, precipitation, and humidity, it is possible to map areas currently or imminently at high risk for disease outbreaks using satellite remote sensing. In this paper we propose the development of an operational geospatial system for malaria and dengue fever early warning; this can be done by bringing together geographic information system (GIS) tools, artificial neural networks (ANN) for efficient pattern recognition, the best available ground-based epidemiological and …

Deriving High-Resolution Protein Backbone Structure Propensities From All Crystal Data Using The Information Maximization Device, Armando D. Solis

Publications and Research

The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), …

Data-Based Perfect-Deficit Approach To Understanding Climate Extremes And Forest Carbon Assimilation Capacity, Suhua Wei, Chuixiang Yi, George Hendrey, Timothy Eaton, Gerald Rustic, Shaoqiang Wang, Heping Liu, Nir Y. Krakauer, Weiguo Wang, Ankur R. Desai, Leonardo Montagnani, Kyaw Tha Paw U, Matthias Falk, Andrew Black, Christian Bernhofer, Thomas Grünwald, Tuomas Laurila, Alessandro Cescatti, Eddy Moors, Rosvel Bracho, Riccardo Valentini

Publications and Research

Several lines of evidence suggest that the warming climate plays a vital role in driving certain types of extreme weather. The impact of warming and of extreme weather on forest carbon assimilation capacity is poorly known. Filling this knowledge gap is critical towards understanding the amount of carbon that forests can hold. Here, we used a perfect-deficit approach to identify forest canopy photosynthetic capacity (CPC) deficits and analyze how they correlate to climate extremes, based on observational data measured by the eddy covariance method at 27 forest sites over 146 site-years. We found that droughts severely affect the carbon assimilation …

A Method To Make A Craniotomy On The Ventral Skull Of Neonate Rodents, Adrián Rodríguez-Contreras, Lingyan Shi, Bingmei M. Fu

Publications and Research

The use of a craniotomy for in vivo experiments provides an opportunity to investigate the dynamics of diverse cellular processes in the mammalian brain in adulthood and during development. Although most in vivo approaches use a craniotomy to study brain regions located on the dorsal side, brainstem regions such as the pons, located on the ventral side remain relatively understudied. The main goal of this protocol is to facilitate access to ventral brainstem structures so that they can be studied in vivo using electrophysiological and imaging methods. This approach allows study of structural changes in long-range axons, patterns of electrical …

Towards Structural Systems Pharmacology To Study Complex Diseases And Personalized Medicine, Lei Xie, Xiaoxia Ge, Hepan Tan, Li Xie, Yinliang Zhang, Thomas Hart, Xiaowei Yang, Philip E. Bourne

Publications and Research

Genome-Wide Association Studies (GWAS), whole genome sequencing, and high-throughput omics techniques have generated vast amounts of genotypic and molecular phenotypic data. However, these data have not yet been fully explored to improve the effectiveness and efficiency of drug discovery, which continues along a one-drug-one-target-one-disease paradigm. As a partial consequence, both the cost to launch a new drug and the attrition rate are increasing. Systems pharmacology and pharmacogenomics are emerging to exploit the available data and potentially reverse this trend, but, as we argue here, more is needed. To understand the impact of genetic, epigenetic, and environmental factors on drug action, …

China’S Water Sustainability In The 21st Century: A Climate-Informed Water Risk Assessment Covering Multi-Sector Water Demands, X. Chen, Naresh Devineni, L. Upmanu, Z. Hao, L. Dong, Q. Ju, J. Wang, S. Wang

Publications and Research

China is facing a water resources crisis with growing concerns as to the reliable supply of water for agricultural, industrial and domestic needs. High inter-annual rainfall variability and increasing consumptive use across the country exacerbates the situation further and is a constraint on future development. For water sustainability, it is necessary to examine the differences in water demand and supply and their spatio-temporal distribution in order to quantify the dimensions of the water risk. Here, a detailed quantitative assessment of water risk as measured by the spatial distribution of cumulated deficits for China is presented. Considering daily precipitation and temperature …

Intelligent Sampling For Big Data Using Bootstrap Sampling And Chebyshev Inequality, Ashwin Satyanarayana

Publications and Research

The amount of data being generated and stored is growing exponentially, owed in part to the continuing advances in computer technology. These data present tremendous opportunities in data mining, a burgeoning field in computer science that focuses on the development of methods that can extract knowledge from data. In many real world problems, these data mining algorithms have access to massive amounts of data. Mining all the available data is prohibitive due to computational (time and memory) constraints. Much of the current research is concerned with scaling up data mining algorithms (i.e. improving on existing data mining algorithms for larger …

Inhibition Of Fatty Acid Binding Proteins Elevates Brain Anandamide Levels And Produces Analgesia, Martin Kaczocha, Mario J. Rebecchi, Brian P. Ralph, Yu-Han Gary Teng, William T. Berger, William Galbavy, Matthew W. Elmes, Sherrye T. Glaser, Liqun Wang, Robert C. Rizzo, Dale G. Deutsch, Iwao Ojima

Publications and Research

The endocannabinoid anandamide (AEA) is an antinociceptive lipid that is inactivated through cellular uptake and subsequent catabolism by fatty acid amide hydrolase (FAAH). Fatty acid binding proteins (FABPs) are intracellular carriers that deliver AEA and related N-acylethanolamines (NAEs) to FAAH for hydrolysis. The mammalian brain expresses three FABP subtypes: FABP3, FABP5, and FABP7. Recent work from our group has revealed that pharmacological inhibition of FABPs reduces inflammatory pain in mice. The goal of the current work was to explore the effects of FABP inhibition upon nociception in diverse models of pain. We developed inhibitors with differential affinities for FABPs to …

Teaching Electrical Circuits Using A Virtual Lab, Md Zahidur Rahman

Publications and Research

This paper describes an engineering professor’s first attempt at designing and implementing a scholarship of teaching and learning (SoTL) study in a basic electrical circuits course at LaGuardia Community College. Inspired by his understanding of Lee Shulman’s (2005) concept of “signature pedagogy” and Eric Mazur’s emphasis on student-centered approaches (2009, November 12), and aware that his students did not always understand the electrical theories and concepts presented in class, the author decided to change his pedagogy. He explains his efforts to train his students to think as engineers, first by making them more “visible” and “accountable” in the classroom, and …