Digital Commons Network^™

A Divisive Shuffling Approach (Vista) For Gene Expression Analysis To Identify Subtypes In Chronic Obstructive Pulmonary Disease, Jörg Menche, Amitabh Sharma, Michael H. Cho, Ruth J. Mayer, Stephen I. Rennard, Bartolome Celli, Bruce E. Miller, Nick Locantore, Ruth Tal-Singer, Soumitra Ghosh, Chris Larminie, Glyn Bradley, John H. Riley, Alvar Agusti, Edwin K. Silverman, Albert-László Barabási

Journal Articles: Pulmonary & Critical Care Med

BACKGROUND: An important step toward understanding the biological mechanisms underlying a complex disease is a refined understanding of its clinical heterogeneity. Relating clinical and molecular differences may allow us to define more specific subtypes of patients that respond differently to therapeutic interventions.

RESULTS: We developed a novel unbiased method called diVIsive Shuffling Approach (VIStA) that identifies subgroups of patients by maximizing the difference in their gene expression patterns. We tested our algorithm on 140 subjects with Chronic Obstructive Pulmonary Disease (COPD) and found four distinct, biologically and clinically meaningful combinations of clinical characteristics that are associated with large gene expression …

Molecular Actions Of The Vitamin D Receptor In Breast Cancer, Erika Laporta

Legacy Theses & Dissertations (2009 - 2024)

1,25-Dihydroxyvitamin D (1,25D) exerts anti-cancer actions through the vitamin D receptor (VDR) but the specific targets that mediate these effects remain to be defined. In these studies, growth and genomic responses to 1,25D were evaluated in a cellular model system derived from mammary tumors generated in VDR knockout (KO) and wildtype (WT) mice. WT145 cells (derived from WT tumors) expressed VDR and were growth inhibited by 1,25D, whereas KO240 cells (derived from VDRKO tumors) lacked VDR and were not growth inhibited by 1,25D. KO240 cell clones stably expressing VDR (KOhVDR cells) were sensitized to 1,25D mediated growth arrest. Genomic profiling …

Community Forests : A Study Of New Hampshire's Town-Owned Forests, Anna Christie-Carnicella

Legacy Theses & Dissertations (2009 - 2024)

New England states have a long history of forest management, beginning in the seventeenth century, with community forests evolving over time from communal forests during colonial times to town-owned forests managed by conservation commissions in the present time. New Hampshire towns provided a case study of the current state of town-owned forest protection and management, with a focus on timber management. I administered a survey to 50 randomly sampled towns and received data from 29 about permanent protection and management activities on town-owned forestland (≥ 50 acres). I used this data, demographic, and landscape data, to evaluate permanent protection and …

When Every Teacher Is A Language Teacher : A Case Study Of High School Math And Science Instructors' Use Of Multimodal Accommodations With Els, Karen Marie Gregory

Legacy Theses & Dissertations (2009 - 2024)

This case study investigated the multimodal accommodations that content teachers make in order to dually support linguistic and conceptual development for English language learning students. Data from digitally recorded classroom observations, teacher interviews, student work, and questionnaires were collected from the participating math and science teachers. The data were analyzed from the theoretical framework of an ecological -semiotic perspective of language teaching and learning (van Lier, 2004), and is theoretically tied to communication accommodation theory and multimodal communication theory as well.

Perfluorinated Compounds, Thyroid Function, And Neuropsychological Status In Older Residents Of Upper Hudson River Communities, Srishti Shrestha

Legacy Theses & Dissertations (2009 - 2024)

Perfluorinated compounds (PFCs) are widespread in the environment. Minimal data exist regarding the neurotoxicity and thyroid disruptive property of PFCs in aging populations and the possible mediating effects of thyroid hormones (THs). In this study, we assessed associations among PFCs, thyroid function, and neuropsychological status, and determined if the neurotoxic effects of PFCs are mediated by changes in THs in an aging population. We measured perfluorooctanoic acid (PFOA), perfluorooctane sulfonate (PFOS), thyroid stimulating hormone (TSH), total thyroxine (T4), free T4 (fT4), and total triiodothyronine (T3) in serum and performed neuropsychological tests in men and women aged 55-74 years and living …

Examining The Risk And Protective Factors That Influence Falls Among Native American Older Adults, Kelly Winjum

Legacy Theses & Dissertations (2009 - 2024)

The risk factors for falls and the adverse outcomes of falls have been well documented among the general older adult population. However, fall frequency, fall risk factors, and fall outcomes have rarely been studied among minority groups specifically. Furthermore, to date there are no known studies that exclusively examine falls among Native American older adults. The purpose of this study is to examine falls among Native American older adults, in order to understand the risk and protective factors for falling among this population, and to develop recommendations for intervention. The theoretical framework of the Disablement Process guides this study. The …

Instructional Scientific Humor In The Secondary Classroom, Francine Wizner

Legacy Theses & Dissertations (2009 - 2024)

This study is an examination of the manner in which educators employ scientific content humor and how that humor is perceived by their students. Content humor is a useful strategy in drawing the attention of students and improving their receptivity toward scientific information. It is also a useful tool in combating the growing distractions of the electronic classroom. Previous studies have found that humor has a positive effect on knowledge, memory, and understanding. However, few studies have been conducted below the undergraduate level and mainly quantitative measures of student recall have been used to measure learning. This study employed multiple …

Medico-Politics And English Literature, 1790-1830 : Immunity, Humanity, Subjectivity, Amy Mallory-Kani

Legacy Theses & Dissertations (2009 - 2024)

In 1796, Dr. Edward Jenner began vaccinating individuals against small pox by using matter from the pustules of the cow pox. Though extremely controversial because of its discomforting mixture of animal and human, by the end of the Romantic period, vaccination was celebrated as the safest way to immunize the British population. Through the practice of vaccination, Britain found a way to save its body politic from a destructive epidemic while affirming the strong connection between individual health and collective well-being that writers of the period like Mary Wollstonecraft, William Wordsworth, Jane Austen, and Mary Shelley recognized in their works. …

Outpatient Treatment Approaches, Services And Outcomes For Older Addicted Adults, Nicole Sarette Macfarland

Legacy Theses & Dissertations (2009 - 2024)

Abstract

Exposure Assessment And Risk Management Of Engineered Nanoparticles : Investigation In Semiconductor Wafer Processing, Michele Shepard

Legacy Theses & Dissertations (2009 - 2024)

Engineered nanomaterials (ENMs) are currently used in hundreds of commercial products and industrial processes, with more applications being investigated. Nanomaterials have unique properties that differ from bulk materials. While these properties may enable technological advancements, the potential risks of ENMs to people and the environment are not yet fully understood. Certain low solubility nanoparticles are more toxic than their bulk material, such that existing occupational exposure limits may not be sufficiently protective for workers. Risk assessments are currently challenging due to gaps in data on the numerous emerging materials and applications as well as method uncertainties and limitations.

Refining Aquatic Macroinvertebrate Community Metrics For The Assessment Of Headwater Streams In New York State, Brian T. Duffy

Legacy Theses & Dissertations (2009 - 2024)

The River Continuum Concept describes the structural and functional shift that occurs from sensitive headwater streams to the lowest reaches of large, non-wadeable rivers. New York State (NYS) maintains a long-established biological monitoring program using macroinvertebrate community assemblages for water quality assessment. However, headwater streams are rarely assessed, and no reference models are available, except those calibrated for lower-continuum wadeable streams and rivers. Current patterns of rural landuse change emphasize the need for more accurate assessment of previously neglected headwaters, in order to set natural reference standards for more accurate assessments of water quality. Ecoregion, drainage area (DA), elevation (elev.), …

A Population-Based Case-Control Study Of The Association Between Extreme Heat Events And Neural Tube Defects And Oral Clefts, Aida Soim

Legacy Theses & Dissertations (2009 - 2024)

With climate change it is expected that extreme weather events will become more frequent and longer in duration. The health consequences of maternal exposure during pregnancy to extreme heat events are not well understood in spite of biological plausibility for adverse effects suggested by prior findings. There is very limited research that explores the relationship between extreme heat events and birth defects. The overall goal of this line of research was to determine whether heatwaves (HW) are associated with two major classes of birth defects: neural tube defects (NTDs) and oral clefts. One component of this project aimed to describe …

The Blackness Of Black (W)Holes, Eric M. Anderson

Legacy Theses & Dissertations (2009 - 2024)

The Blackness of Black (W)holes analyzes Toni Morrison's Sula, William Faulkner's Sanctuary, and Ralph Ellison's Invisible Man as against establishing the illusion of a coherent, recognizable self through relational identities and subservience to denotative language and categories of identity. These novel’s feature characters packing knives, I claim, because they advocate for what I term stylistic self–extrication: a rupture with prevailing forms of identity and cliché ways of speaking through rhythmic, sonorous, experimental language use. Characters who succeed at the task, I argue, are associated with a blackness in excess of racial markings, because they become unclassifiable as a result. In …

Computational Modeling-Driven Study Of Signaling Pathway Affecting Cleft Formation During Submandibular Salivary Gland Development, Shayoni Ray

Legacy Theses & Dissertations (2009 - 2024)

Branching morphogenesis is a conserved mechanism of mammalian organ development (salivary glands, lungs, mammary glands, pancreas, kidney, etc.), and has been a classic topic of study for generations of developmental biologists. During the process of tissue formation, several cellular and molecular and protein signaling events occur at successive stages enabling proper formation of tissue shape and structure. In order to provide a comprehensive understanding of the process of branching morphogenesis, we need a systems level approach to integrate multifactorial information. My overall global hypothesis is that multiple mathematical modeling approaches can be utilized to extract crucial cellular and tissue level …

Uncovering Organosulfur Natural Products In The "Shy-Plant" Mimosa Pudica Via Direct Analysis In Real Time Mass Spectrometry : Volatiles Emission From Touch Sensitive Roots, Max Jacob Maron

Legacy Theses & Dissertations (2009 - 2024)

Mimosa pudica L. (Mimosaceae) is a small shrub endemic to South America, now pantropically distributed. M. pudica displays the properties of seismonasty where the leaves fold and stems droop in response to both touch, as well as nyctinasty, a type of circadian rhythm. It was previously reported that the principal component of the odor that is produced when M. pudica is uprooted is caused by CS2 and COS, both of which were detected by GC-MS. The present study has found that the roots emit a foul odor in response to direct root stimulation. Further, neither CS2 nor COS were observed …

A Structural And Functional Comparison Of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein (Ncp7) And Other Retroviral Nucleocapsid Proteins, Christopher Richard Cavender

Legacy Theses & Dissertations (2009 - 2024)

Human immunodeficiency virus type 1 (HIV-1) is a retrovirus belonging to the lentivirus genus of the orthoretrovirinae family. HIV-1 is widely known for causing acquired immunodeficiency syndrome (AIDS) in humans and being responsible for 1.8 million deaths due to AIDS associated illnesses in 201016.

Mouse Salivary Gland Development Requires Optimal Substrate Compliance, Sarah Beth Peters

Legacy Theses & Dissertations (2009 - 2024)

The embryonic mouse submandibular salivary gland (mSMG) is a classic model to study mechanochemical signals involved in morphogenesis and differentiation amongst multiple, interacting cell populations. Scaffold compliance is alters cellular phenotype, but little is known about the effects of compliance on organogenesis. The overall aim of this project was to demonstrate that the processes of salivary gland epithelial branching morphogenesis and differentiation require a compliant, in vivo-like environment and are disrupted outside of this range.

Coping With Negative Emotion In Middle Childhood : Relationship To Temperament And Psychopathology, Kristen Uhl

Legacy Theses & Dissertations (2009 - 2024)

Children are exposed to various stressors throughout development. Research has demonstrated that childhood stressors can negatively affect adjustment, and that children's temperament and coping impact the effects of stress on adjustment. The current study examines children's coping responses to situations eliciting anger, sadness, fear, and worry in a sample of 191 children (102 boys, 89 girls; mean age = 9.57 years, SD=0.57) recruited from a suburban school district. Additionally, the predictive relationship of temperament variables on coping strategy use is explored. Finally, coping and temperament's effect on the development of psychopathology is investigated. Results show that children reported using more …

Power Law Models Of Stock Indices, Mankit Tse

Legacy Theses & Dissertations (2009 - 2024)

Viewing the stock market as a self-organized system, Sornette and Johansen introduced physics-based models to study the dynamics of stock market crashes from the perspective of complex systems. This involved modeling stock market Indices using a mathematical power law exhibiting log-periodicity as the system approaches a market crash, which acts like a critical point in a thermodynamic system. In this dissertation, I aim to investigate stock indices to determine whether or not they exhibit log-periodic oscillations, according to the models proposed by Sornette, as they approach a crash. In addition to analyzing stock market crashes in the frequency domain using …

Effects Of Acute Stress And Gender On Decision-Making, Stephanie Elaine Wemm

Legacy Theses & Dissertations (2009 - 2024)

The current study examined the effects of a social stressor on subsequent performance on the Iowa Gambling Task (IGT), and the role of sex on this relationship. Fifty-six participants (24 men and 32 women) were assigned randomly to a social stressor (Trier Social Stress Test) or a control condition while their subjective emotional reactions and their physiological arousal (skin conductance and heart rate) were measured. Findings showed that participants in the stress condition responded with higher skin-conductance levels and heart rate during the social stressor, in addition to reporting greater negative affect directly following the social stressor. They also made …

Biomacromolecule Conjugated Nanofiber Scaffold For Salivary Gland Tissue Engineering, Kavitha Jayarathanam

Legacy Theses & Dissertations (2009 - 2024)

ABSTRACT :

The Sex Ratio, Gender Equality, And Women's Victimization : A Cross-National Analysis, Laura M. Demarco

Legacy Theses & Dissertations (2009 - 2024)

The relationship between the sex ratio and crime is underdeveloped in the criminological literature, particularly regarding the victimization of women. Much of the existing work draws on theorizing by Guttentag and Secord (1983) on the interpersonal dynamics related to dyadic power. In this line of research, the characteristics of structural power are largely taken for granted. Drawing on literature about gender inequality and women's victimization, this study recasts Guttentag and Secord's notion of structural power as a continuous measure of gender equality. I examine the effect of the sex ratio on women's victimization, and evaluate if that effect is contingent …

Risk Classification’S Big Data (R)Evolution, Rick Swedloff

Connecticut Insurance Law Journal

Insurers can no longer ignore the promise that the algorithms driving big data will offer greater predictive accuracy than traditional statistical analysis alone. Big data represents a natural evolutionary advancement of insurers trying to price their products to increase their profits, mitigate additional moral hazard, and better combat adverse selection. But these big data promises are not free. Using big data could lead to inefficient social and private investments, undermine important risk-spreading goals of insurance, and invade policyholder privacy. These dangers are present in any change to risk classification. Using algorithms to classify risk by parsing new and complex data …

Information & Equilibrium In Insurance Markets With Big Data, Peter Siegelman

Connecticut Insurance Law Journal

Asymmetric information makes the behavior of insurance markets very difficult to predict. But this Article argues that the increasing use of Big Data by insurers will not result in forecasts of loss that are so accurate that they eliminate uncertainty, and with it, the possibility of insurance. Big Data techniques might lead to a “flip” in informational asymmetry, resulting in a situation in which insurers know more about their customers than the latter know about themselves. But the effects of such a development could actually be benign. Finally, the Article considers the potential for Big (or at least, More) Data …

Southern Flounder (Paralichthys Lethostigma) Stock Structure Inferred From Otolith Shape Analysis, Stephen R. Midway, Steven X. Cadrin, Frederick S. Scharf

Biology

Examination of otolith morphometric variation has been shown to provide improved descriptions of stock structure for several marine fish species. We examined spatial variation in otolith shape of southern flounder (Paralichthys lethostigma) to understand population structure at the following geographic levels: ocean basin (Atlantic and Gulf of Mexico); regional coastal waters (Texas, Florida) and (Georgia, South Carolina); and local coastal waters (North Carolina). To reduce variability, we considered only age- 1 female fish. From digitized otolith images, we extracted descriptions for common shape indices and elliptical Fourier coefficients and found strong evidence for differences at the ocean basin scale, but …

The Ubiquitin-Proteasome Pathway Protects Chlamydomonas Reinhardtii Against Selenite Toxicity, But Is Impaired As Reactive Oxygen Species Accumulate, Patrick Vallentine, Chiu Yueh Hung, Jiahua Xie, Doug Van Hoewyk

Biology

The ubiquitin-proteasome pathway (UPP) coordinates a myriad of physiological processes in higher plants, including abiotic stress responses, but it is less well characterized in algal species. In this study, the green alga Chlamydomonas reinhardtii was used to gain insights into the role of the UPP during moderate and severe selenite stress at three different time points. The data indicate that activity of the UPP in response to selenium (Se) stress was both time and dose dependent. Moderate selenite stress increased proteasome activity, protein ubiquitination and the proteasomal removal of malformed selenoproteins. However, severe Se stress caused by prolonged selenite treatment …

Correlation Of Ischemia-Modified Albumin With Sofa And Apache Ii Scores In Preoperative Patients With Colorectal Cancer, Masaaki Katoh, Kazuhiko Kotani, Alejandro Gugliucci, Hisanaga Horie, Russell Caccavello, Mamoru Takeuchi

Faculty Publications & Research of the TUC College of Osteopathic Medicine

Purpose. Critical illnesses are assessed according to the sequential organ failure assessment (SOFA) and acute physiology and chronic health evaluation (APACHE) II. Circulating ischemia-modified albumin (IMA) is a biomarker generated under ischemic and oxidative conditions and may reflect disease severity in preoperative patients. This study investigated the correlations of IMA with SOFA and APACHE II scores in inpatients admitted for colorectal surgery. Methods.We examined 27 patients with advanced colorectal cancers (mean age 69 years, men/women = 15/12). Correlations between SOFA and APACHE II scores in addition to preoperative serum IMA and C-reactive protein (CRP) levels were analyzed. Results …

The Evolutionary Fitness Of Personality Traits In A Small-Scale Subsistence Society, Michael Gurven, Christopher Von Rueden, Jonathan Stieglitz, Hillard Kaplan, Daniel Eid Rodriguez

ESI Publications

"Personality, or “behavioral syndromes”, are relatively stable dispositional traits and behaviors that have now been identified in a myriad of social species (Gosling, 2001; Sih et al., 2004), and with clear consequences on fitness (Smith & Blumstein, 2008). The canalization of personality during development and relative stability thereafter, despite varying circumstances over the life course that might otherwise favor greater plasticity, is an important problem attracting much theoretical and empirical attention (Dall et al., 2004; Dingemanse et al., 2010). Further, personality is highly heritable, yet how heritable genetic variation in personality traits is maintained over generations remains another conundrum (Buss …

Engineering Liposomes, Ushna Vaid

Honors Capstones

The purpose is to design and evaluate the liposomal formulations to overcome disadvantages such as short half-life, prone to oxidation and hydrolysis, leakage and fusion in vitro. Liposomes are prepared using different techniques like lipid hydration and extrusion, reverse phase evaporation, ethanol injection, sonication, ethanol destabilization and mannitol freeze thaw methods. The formulations made using each of these methods were evaluated based on particle size and encapsulation efficiency. The particle size was measured using Dynamic light scattering and the encapsulation efficiency was measured using fluorescence spectroscopy. Finally, the suitable formulations were tested for dye release studies using SOT AX dissolution …

Nanoparticle Encapsidation Of Flock House Virus By Auto Assembly Of Tobacco Mosaic Virus Coat Protein, Payal D. Maharaj, Jyothi K. Mallajosyula, Gloria Lee, Phillip Thi, Yiyang Zhou, Christopher M. Kearney, Alison A. Mccormick

Faculty Publications & Research of the TUC College of Pharmacy

Tobacco Mosaic virus (TMV) coat protein is well known for its ability to self-assemble into supramolecular nanoparticles, either as protein discs or as rods originating from the ~300 bp genomic RNA origin-of-assembly (OA). We have utilized TMV self-assembly characteristics to create a novel Flock House virus (FHV) RNA nanoparticle. FHV encodes a viral polymerase supporting autonomous replication of the FHV genome, which makes it an attractive candidate for viral transgene expression studies and targeted RNA delivery into host cells. However, FHV viral genome size is strictly limited by native FHV capsid. To determine if this packaging restriction could be eliminated, …