Digital Commons Network^™

Elucidation Of How Cancer Cells Avoid Acidosis Through Comparative Transcriptomic Data Analysis, Kun Xu

School of Computing: Faculty Publications

The rapid growth of cancer cells fueled by glycolysis produces large amounts of protons in cancer cells, which tri mechanisms to transport them out, hence leading to increased acidity in their extracellular environments. It has been well established that the increased acidity will induce cell death of normal cells but not cancer cells. The main question we address here is: how cancer cells deal with the increased acidity to avoid the activation of apoptosis. We have carried out a comparative analysis of transcriptomic data of six solid cancer types, breast, colon, liver, two lung (adenocarcinoma, squamous cell carcinoma) and prostate …

Computational Prediction Of Human Salivary Proteins From Blood Circulation And Application To Diagnostic Biomarker Identification, Jiaxin Wang, Yanchun Liang, Yan Wang, Juan Cui, Ming Liu, Wei Du, Ying Xu

School of Computing: Faculty Publications

Proteins can move from blood circulation into salivary glands through active transportation, passive diffusion or ultrafiltration, some of which are then released into saliva and hence can potentially serve as biomarkers for diseases if accurately identified. We present a novel computational method for predicting salivary proteins that come from circulation. The basis for the prediction is a set of physiochemical and sequence features we found to be discerning between human proteins known to be movable from circulation to saliva and proteins deemed to be not in saliva. A classifier was trained based on these features using a support-vector machine to …

Multilayered Plasmonic Covers For Comblike Scattering Response And Optical Tagging, Francesco Monticone, Christos Argyropoulos, Andrea Alu

Department of Electrical and Computer Engineering: Faculty Publications

We discuss the potential of multilayered plasmonic particles to tailor the optical scattering response. The interplay of plasmons localized in thin stacked shells realizes peculiar degenerate cloaking and resonant states occurring at arbitrarily close frequencies. These concepts are applied to realize ultrasharp comblike scattering responses and synthesize staggered, ideally strong superscattering states closely coupled to invisible states. We demonstrate robustness to material losses and to variations in the background medium, properties that make these structures ideal for optical tagging.

Effects Of Heat Stress On Oocyte Quality And Embryo Viability In Swine, Andrew Miller

Open Access Theses

Heat stress during oocyte maturation causes well-defined changes in the oocyte cytoplasm that leads to reduced developmental potential. Previous work has been done that supports this hypothesis, but the underlying reasons are still not fully understood. Our objective is to determine these underlying mechanisms that contribute to this reduction in overall development potential of the oocytes and the embryos. Oocytes underwent in vitro maturation (IVM) for 40-44 hours in one of two environments: 39°C (control), or 41°C (heat stress). The oocytes underwent multiple experiments: stage of meiosis after maturation, endoplasmic reticulum (ER) size, total amount of Ca2+ stored in the …

Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia

Publications

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output …

Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov

Publications

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to …

Between Algorithm And Model: Different Molecular Surface Definitions For The Poisson-Boltzmann Based Electrostatic Characterization Of Biomolecules In Solution, Sergio Decherchi, José Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, Walter Rocchia

Publications

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric …

Enduring Quests - Daring Visions (Nasa Astrophysics In The Next Three Decades), Dieter H. Hartmann

Publications

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Chlorine Dioxide Gas Treatment Of Cantaloupe And Residue Analysis, Simran Kaur

Open Access Theses

Chlorine dioxide is a selective oxidant and powerful antimicrobial agent. Previous work has shown that treatment of cantaloupe with chlorine dioxide gas at 5 mg/L for 10 minutes results in a 4.6 and 4.3 log reduction of E. coli O157:H7 and L. monocytogenes respectively. A significant reduction (p

Current analytical methods for chlorine dioxide and chloroxyanions are only applicable to aqueous samples. Some of these methods have been used to determine surface residues in treated products by analyzing rinse-water. In order to quantify residues in the tissues of a more complex food matrix, while reducing interference from natural organic matter, …

Hare And Tortoise: How Do Price Change Patterns Affect Propensity To Book, Zhuoyang Li

Open Access Theses

With an increasing using of online booking, hotel room rate changing information becomes nearly transparent to consumers. And this trend encourages deal-seeking consumer behaviors, which are based on price change information. So hotels can influence consumers' propensity to book through managing price changes. The present study aims at examining consumers' propensity to book in a more realistic context by introducing two conditions: different price changing patterns and interaction between price-moving trends and price patterns. It is important for hotel managers to understand the impact of different price change trends and patterns because price changes can directly affect consumer perception and …

Improving Farm Management Decisions By Analyzing Production Expenditure Allocations And Farm Performance Standing, William A. Osborne

Theses and Dissertations--Agricultural Economics

This study examines the potential effects of categorical increases in production expenditures on farm income performance according to farm standing. The objective of this study is to expose differences in anticipated net farm income return from production expenditure investments and the optimal expense allocation strategy for each performance level. Studying farm performance through segregation by utilizing a two-tier analysis and quantile regression acknowledges the possibility that managerial strategy can differ based on managerial ability. Study outcomes are useful to farm managers because they offer more prescription style results and interpretations than found in other farm performance studies. Study findings show …

Inclusion And Exclusion In Some Feminist Utopian Fictions, Karen F. Stein

English and Creative Writing Faculty Publications

No abstract provided.

Proline Mechanisms Of Stress Survival, Xinwen Liang, Lu Zhang, Sathish Kumar Natarajan, Donald F. Becker

Department of Biochemistry: Faculty Publications

Significance: The imino acid proline is utilized by different organisms to offset cellular imbalances caused by environmental stress. The wide use in nature of proline as a stress adaptor molecule indicates that proline has a fundamental biological role in stress response. Understanding the mechanisms by which proline enhances abiotic/biotic stress response will facilitate agricultural crop research and improve human health. Recent Advances: It is now recognized that proline metabolism propels cellular signaling processes that promote cellular apoptosis or survival. Studies have shown that proline metabolism influences signaling pathways by increasing reactive oxygen species (ROS) formation in the mitochondria …

Creating A Campus One Lot At A Time, Edgar Luecke

Engineering Faculty Publications, Patents, Presentations

No abstract provided.

Releasing Privilege: How Can We Develop Indigenous Knowledge In Our Classrooms?, Suzanne Jenkins

Arts Conference Papers

Historically research, theory and practice has focussed on promoting and maintaining Western privilege through Western knowledge and Western ways of knowing that deny the validity of Indigenous knowledge and culture. Psychology, in particular, has been complicit in the colonising process and, as a dominant discourse, has a documented past that has been ethnocentric and has objectified, dehumanised and devalued those from culturally different groups (McLeod, 1997; Nystul, 2011). As non-Indigenous professionals, central to our ability to act as effective cultural allies will be how we can form meaningful alliances with our Indigenous students/clients. To be successful we need to develop …

Vol. 25 No. 1 Semester 1 (2013)

In Principio - 2010s

No abstract provided.

Vlincrnas Controlled By Retroviral Elements Are A Hallmark Of Pluripotency And Cancer, Georges St. Laurent, Dmitry Shtokalo, Biao Dong, Michael R. Tackett, Xiaoxuan Fan, Sandra Lazorthes, Estelle Nicolas, Nianli Sang, Timothy J. Triche, Timothy A. Mccaffrey, Wendiong Xiao, Philipp Kapranov

Medicine Faculty Publications

Background

The function of the non-coding portion of the human genome remains one of the most important questions of our time. Its vast complexity is exemplified by the recent identification of an unusual and notable component of the transcriptome - very long intergenic non-coding RNAs, termed vlincRNAs.

Results

Here we identify 2,147 vlincRNAs covering 10 percent of our genome. We show they are present not only in cancerous cells, but also in primary cells and normal human tissues, and are controlled by canonical promoters. Furthermore, vlincRNA promoters frequently originate from within endogenous retroviral sequences. Strikingly, the number of vlincRNAs expressed …

Bone-Targeted Therapies In Metastatic Castration-Resistant Prostate Cancer: Evolving Paradigms, Joelle El-Amm, Ashley Freeman, Nihar Patel, Jeanny B. Aragon-Ching

Medicine Faculty Publications

Majority of patients with metastatic castrate resistant prostate cancer (mCRPC) develop bone metastases which results in significant morbidity and mortality as a result of skeletal-related events (SREs). Several bone-targeted agents are either in clinical use or in development for prevention of SREs. Bisphosphonates were the first class of drugs investigated for prevention of SREs and zoledronic acid is the only bisphosphonate that is FDA-approved for this indication. Another bone-targeted agent is denosumab which is a fully humanized monoclonal antibody that binds to the RANK-L thereby inhibiting RANK-L mediated bone resorption. While several radiopharmaceuticals were approved for pain palliation in mCRPC …

Genomic Profiling Reveals The Potential Role Of Tcl1a And Mdr1 Deficiency In Chemotherapy-Induced Cardiotoxicity, Timothy A. Mccaffrey, Constantine Tziros, Jannet Lewis, Richard Katz, Robert S. Siegel, William B. Weglicki, Jay H. Kramer, I. Tong Mak, Ian Toma, Liang Chen, Elizabeth Benas, Alexander Lowitt, Shruti Rao, Linda Witkin, Yi Lian, Zhaoqing Yang, Sidney W. Fu

Medicine Faculty Publications

Background: Anthracyclines, such as doxorubicin (Adriamycin), are highly effective chemotherapeutic agents, but are well known to cause myocardial dysfunction and life-threatening congestive heart failure (CHF) in some patients.

Methods: To generate new hypotheses about its etiology, genome-wide transcript analysis was performed on whole blood RNA from women that received doxorubicin-based chemotherapy and either did, or did not develop CHF, as defined by ejection fractions (EF)≤40%. Women with non-ischemic cardiomyopathy unrelated to chemotherapy were compared to breast cancer patients prior to chemo with normal EF to identify heart failure-related transcripts in women not receiving chemotherapy. Byproducts of oxidative stress in plasma …

Biclonal Gammopathy In A Patient Taking Efalizumab For The Treatment Of Psoriasis, Antonia Fthenakis, Kurt S. Wenk, Alison Ehrlich, Jeanny B. Aragon-Ching

Dermatology Faculty Publications

We report a patient who developed biclonal gammopathy of undetermined significance during treatment with
efalizumab for psoriasis. This plasma cell disorder was found during the evaluation of the patient’s complaint of mild lower extremity paresthesia. The gammopathy spontaneously remitted following cessation of therapy and has not recurred to date. Given the increasing use and development of biological agents for the treatment of psoriasis and other disorders, this finding and the mechanisms by which it may have occurred is of clinical significance.

Dux4 Expression In Fshd Muscle Cells: How Could Such A Rare Protein Cause A Myopathy?, Alexandra Tassin, Dalila Laoudj-Chenivesse, Celine Vanderplanck, Marietta Barro, Sebastien Charron, Eugenie Ansseau, Yi-Wen Chen, Jacques Mercier, Frederique Coppee, Alexandra Belayew

Genomics and Precision Medicine Faculty Publications

Facioscapulohumeral muscular dystrophy (FSHD) is one of the most frequent hereditary muscle disorders. It is linked to contractions of the D4Z4 repeat array in 4q35. We have characterized the double homeobox 4 (DUX4) gene in D4Z4 and its mRNA transcribed from the distal D4Z4 unit to a polyadenylation signal in the flanking pLAM region. It encodes a transcription factor expressed in FSHD but not healthy muscle cells which initiates a gene deregulation cascade causing differentiation defects, muscle atrophy and oxidative stress.PITX1 was the first identified DUX4 target and encodes a transcription factor involved in muscle atrophy. DUX4 was …

Highlights From The Functional Single Nucleotide Polymorphisms Associated With Human Muscle Size And Strength Or Famuss Study, Linda S. Pescatello, Joseph M. Devaney, Monica J. Hubal, Paul D. Thompson, Eric P. Hoffman

Genomics and Precision Medicine Faculty Publications

The purpose of the Functional Single Nucleotide Polymorphisms Associated with Human Muscle Size and Strength study or FAMuSS was to identify genetic factors that dictated the response of health-related fitness phenotypes to resistance exercise training (RT). The phenotypes examined were baseline muscle strength and muscle, fat, and bone volume and their response to RT. FAMuSS participants were 1300 young (24 years), healthy men (42%) and women (58%) that were primarily of European-American descent. They were genotyped for ~500 polymorphisms and completed the Paffenbarger Physical Activity Questionnaire to assess energy expenditure and time spent in light, moderate, and vigorous intensity habitual …

Middle Ear Myoclonus: Two Informative Cases And A Systematic Discussion Of Myogenic Tinnitus, Aviva Ellenstein, Nadia Yusuf, Mark Hallett

Neurology Faculty Publications

Background: The term middle ear myoclonus (MEM) has been invoked to explain symptoms of tinnitus presumably caused by the dysfunctional movement of either of the two muscles that insert in the middle ear: tensor tympani and stapedius. MEM has been characterized through heterogeneous case reports in the otolaryngology literature, where clinical presentation is variable, phenomenology is scarcely described, the pathogenic muscle is usually not specified, natural history is unknown, and the presumptive definitive treatment, tensor tympani or stapedius tendon lysis, is inconsistently effective. It is not surprising that no unique acoustogenic mechanism or pathophysiologic process has been identified to explain …

Personal Reflections From Eportfolio: Ahrc New York City, Dominic Dibiase

Community Action Forum: Seidenberg School

No abstract provided.

Children With Special Health Care Need’S Association Of Passive Tobacco Smoke Exposure And Dental Caries: 2007 National Survey Of Children’S Health, R Constance Wiener

Faculty & Staff Scholarship

Purpose: The purpose of this study was to determine a relationship between passive tobacco smoke exposure (secondhand and third hand tobacco smoke exposure) and dental caries in Children with Special Health Care Needs (CSHCN) ages 0-17 years.

Method: This study used data from the 2007 National Survey of Children’s Health involving 17,901 CSHCN. Telephone survey data were used to determine recent caries experience and passive tobacco smoke exposure (secondhand and third hand tobacco smoke exposure). Recent caries was defined as a positive response to if CSHCN had “decayed teeth or cavities within the past 6 months.” Passive smoke was defined …

Remaining Silent After Salinas, Brandon L. Garrett

University of Chicago Law Review Online

No abstract provided.

Information Collection, United States Army

United States Army: Field Manuals

Information Collection, United States Army Field Manual FM 3-55

Synthesis And Characterization Of A Biometric Model Of The Tricopper Binding Site Of Multicopper Oxidases, Haosen Wang

Honors Theses, 1963-2015

This research employs the principles of bioinorganic modeling, simplifying the extraneous structures of the molecule being mimicked and focusing only on the active components of the large biological molecules. Specifically, this project attempts to mimic the structure and reactivity of tri-copper active sites found in Multi-copper Oxidises, such as Laccase and Ceruloplasmin, that bind with oxygen and reduce it to water. After experimenting with various other structures that failed to mimic the active sites, we selected another potential ligand, 1,3,5-tri(2-pyridylmethyltriazole)-2,4,6-triethyl benzene, abbreviated L_tapma, to be the substrate for this research to bind with three Cu(I) ions and then …

The Control Of Crawling Movement By Interneuron Circuits Of The Drosophila Larva, Mary Sweet

Honors Theses, 1963-2015

The organization of the human brain is extremely complex. Therefore, scientists have relied upon model organisms like the fruit fly Drosophila melanogaster for nervous system studies, because these organisms are less complex and can be experimentally manipulated with genetic tools. In this study, we focus on fruit fly larval crawling behavior and how it can be altered by the manipulation of subsets of neurons that may be involved in generating crawling behavior. Eight subsets were tested and all of them were found to limit normal larval crawling behavior to some degree. The elucidation of these subsets will help us to …

With One Breath, Jessica Solfest

Honors Theses, 1963-2015

Biologists know that the cardiovascular and respiratory systems interact and coordinate via the baroreflex and other pathways, but there is still much to discover regarding the dynamical aspects of their communication. Synchronization patterns between the respiratory and cardiovascular systems evince their interaction. This thesis focuses on the synchronization of cardiovascular and respiratory activity. I analyze the frequency of this synchrony to determine patterns and characterize the systems’ adaptability to changes in the environment. I applied time series analysis and Markov processes to dynamical systems in an attempt to unearth meaning behind cardiorespiratory communicative mysteries. Through this research, I found that …