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Hiv-1 Subtype A Gag Variability And Epitope Evolution, Syed Hani Abidi, Marcia L. Kalish, Farhat Abbas, Sarah Rowland-Jones, Syed Ali

Section of Urology

Objective: The aim of this study was to examine the course of time-dependent evolution of HIV-1 subtype A on a global level, especially with respect to the dynamics of immunogenic HIV gag epitopes.
Methods: We used a total of 1,893 HIV-1 subtype A gag sequences representing a timeline from 1985 through 2010, and 19 different countries in Africa, Europe and Asia. The phylogenetic relationship of subtype A gag and its epidemic dynamics was analysed through a Maximum Likelihood tree and Bayesian Skyline plot, genomic variability was measured in terms of G → A substitutions and Shannon entropy, and the time-dependent …

Interspecific Variation In Juvenile Snapper Otolith Chemical Signatures In The Northern Gulf Of Mexico, William F. Patterson Iii, Beverly K. Barnett, Michelle Zapp Sluis, James Howan Cowan Jr., Alan M. Shiller

Faculty Publications

The objective of this study was to evaluate whether age-0 lane snapper Lutjanus synagris otolith chemical signatures could serve as accurate proxies for those of its congener, red snapper L. campechanus, among northern Gulf of Mexico (GOM) nursery regions. Red (n = 90) and lane (n = 53) snappers were sampled from 3 regions of the northern GOM in fall 2005, and their otolith chemistry was analyzed with sector field-inductively coupled plasma-mass spectrometry (Ba:Ca, Mg:Ca, Mn:Ca, Sr:Ca, Li:Ca) or stable isotope ratio-mass spectrometry (δ¹³C and δ¹⁸O). Chemical signatures were significantly different among regions (MANOVA, p < 0.001) and between species (MANOVA, p = 0.029), with the species effect being driven by significant differences in 4 of the 7 constituents analyzed (ANOVA, p < 0.036). The significant region effect persisted (MANOVA, p < 0.001), but the species effect was non-significant (MANOVA, p = 0.964) when constituent values were normalized to species-specific means. Mean regional classification accuracies from linear discriminant functions computed with otolith constituent data were 84% for lane snapper and 80% for red snapper whether data were normalized or not. Maximum likelihood models parameterized with normalized lane snapper otolith chemistry data estimated red snapper regional composition reasonably well among mixed-region samples (mean error = 9.7% among models). Therefore, it appears age-0 lane snapper otolith chemical signatures can serve as accurate proxies for those of red snapper in the northern GOM. These results have broader implications for deriving natural tags based on otolith chemistry for fishes that may have low abundance in parts of their range.

Biomechanical Properties Of Hemlocks: A Novel Approach To Evaluating Physical Barriers Of The Plant-Insect Interface And Resistance To A Phloem-Feeding Herbivore, Paul Ayayee, Fuqian Yang, Lynne K. Rieske

Entomology Faculty Publications

Micromechanical properties that help mediate herbivore access may be particularly important when considering herbivorous insects that feed with piercing-sucking stylets. We used microindentation to quantify the micromechanical properties of hemlock, Tsuga spp., to quantify the hardness of the feeding site of the invasive hemlock woolly adelgid, Adelges tsugae. We measured hardness of the hemlock leaf cushion, the stylet insertion point of the adelgid, across four seasons in a 1 y period for four hemlock species growing in a common garden, including eastern, western, mountain, and northern Japanese hemlocks. Leaf cushion hardness was highest in the fall and winter and …

Altmetrics Is An Indication Of Quality Research Or Just Hot Topics, Chia Yew Boon, Joan Wee Jee Foon

Proceedings of the IATUL Conferences

With the widespread use of social media tools in the discovery, dissemination and discussion of research output, altmetric measurements are fast gaining popularity and they supplement the traditional research metrics by tracking the number of social mentions of research articles. In recent years, there a few such tools and they adopt different models and have different coverage. Publishers such as Scopus and PLoS have already incorporated altmetrics in their websites. This paper seeks to make sense of these available tools and evaluate their effectiveness. Do they identify quality research or just HOT topics? This paper also analyses most cited papers …

Mendeley As A Source Of Readership By Students And Postdocs? Evaluating Article Usage By Academic Status, Stefanie Haustein, Vincent Larivière

Proceedings of the IATUL Conferences

This paper explores readership counts provided by the social reference manager Mendeley as a source for usage statistics for scientific papers, based on a sample of 1.2 million documents published in journals from the four disciplines Biomedical Research, Clinical Medicine, Health and Psychology. It is shown that the percentage of papers with at least one user on Mendeley (65.9%) as well as the average number of readers per document (9.6) is quite high compared to the uptake and average activity on other social media platforms. The majority of users are PhD and postgraduate students as well as postdocs. Correlations with …

Comparing Nmes Stimulation Intensity At Various Lengths Of The Tibialis Anterior, Brent Brookbush, Maya Hakami, Jennifer Wolff, Amy Zelin

Dissertations, Theses, and Capstone Projects

The purpose of this study was to determine if placement of electrodes at various distances along the Tibialis Anterior muscle belly had a significant effect on the intensity of stimulation needed to evoke a contraction using neuromuscular electrical stimulation (NMES). Twenty subjects between the ages of 21-65 in good health and presented with no precautions to NMES were recruited from the CUNY Hunter College physical therapy department. Two reference lines were drawn on subjects’ legs, one outlining the tibial crest (L1), and another from the most lateral portion of the tibial plateau to the center of the lateral malleolus (L2). …

The Influence Of Naive And Media-Informed Beliefs On Juror Evaluations Of Forensic Science Evidence, Victoria Zoe Lawson

Dissertations, Theses, and Capstone Projects

The National Academy of Sciences (2009) concluded that with the exception of nuclear DNA, none of the forensic sciences has been scientifically validated. It is not clear, however, that people are aware of these deficiencies. Indeed, people tend to think quite highly of forensic science, and find it to be convincing trial evidence. It is not clear to what extent their erroneous beliefs about validity influence the weight given to such evidence, or how best to challenge these beliefs. In the present research, I examined people's beliefs about forensic science and how their beliefs influenced their evaluations of forensic evidence. …

Promoting Wellness Through Mindfulness-Based Activities, Malgorzata Powietrzynska

Dissertations, Theses, and Capstone Projects

The central idea of this dissertation is mindfulness framed as a sociocultural, secular, and multidimensional construct involving attention that is purposeful, in the present moment, and non-judgmental. Mindfulness represents a unification of century-old contemplative Eastern traditions (including Buddhism) and the recent developments of modern, Western science. Hence, supported by the emerging scientific evidence, I argue that mindfulness practices have a potential to offer a wide range of benefits related to wellness. In particular, I report on our hermeneutic-phenomenological studies investigating the centrality of emotions in teaching and learning. Our findings confirm that when adopted in education, mindfulness may mediate positive …

Neoliberalism And The "Obesity Epidemic", Dianne Rubinstein

Dissertations, Theses, and Capstone Projects

Neoliberalism has been described as a political and economic theory that proposes "human well-being can best be advanced by liberating... freedoms...within an institutional framework [of]...strong private property rights [and] free markets.... [I]f markets do not exist (...such as in... health care) then they must be created, by state action if necessary." I would argue that the "Obesity Epidemic" is just such a created Neoliberal market, and in fact does not actually exist as an "epidemic." By changing the computation of BMI (Body Mass Index) in 1998, the federal government created the "Obesity Epidemic" by definitional fiat, despite myriad contradictory evidence

How Silently Sheela-Na-Gig Speaks: Memory, Mythos, And The Female Body, Amber C. Snider

Dissertations, Theses, and Capstone Projects

How and why do we destroy female agency, still today? Focusing on some of the mythical foundations and formations found in ancient Celtic and Greek imaginings, the "bodily" aspects in particular, this thesis traces the ways in which some of the modern women intellectuals receive or reject the typical feminist or female elements found in mythologies; the elided nature of the female trinity and the life giver-destroyer circularity inherent in goddesses and archetypes, for instance, appears to mirror our cultural impulse to destroy the female body. It is then not enough to create a new mythology by and for women--we …

The Moral Philosophy Of William Wollaston, Yael Sofaer

Dissertations, Theses, and Capstone Projects

This dissertation provides the first thorough exposition of the moral theory proposed by William Wollaston in his treatise The Religion of Nature Delineated (1724), and demonstrates it to be an innovative contribution to the seventeenth and eighteenth centuries' project of developing a moral theory by reason alone (in which lie the origins of contemporary moral realism); with the foundational principle of acting in accordance with nature as the standard of morality. Wollaston's treatise contains an unrecognized innovation: the principle that rational agents express propositions by their actions--that, as propositions, have truth values--which makes it possible to determine the moral status …

Variation In Habitat Thresholds: An Analysis Of Minimum Habitat Requirements Of North American Breeding Birds, Yntze Van Der Hoek

Dissertations, Theses, and Capstone Projects

Many species show dramatic changes in population extinction or persistence probability at particular habitat amounts. These `extinction thresholds' could be translated to conservation targets, under the condition that we can derive generalities. I investigated the level of variation in landscape-level habitat thresholds for a suite of North American, forest-associated, breeding birds. Records from Breeding Bird Atlases and the availability of remotely-sensed land cover data allowed me to compare habitat thresholds for 25 species across the states of Massachusetts, Michigan, New York, Ohio, Pennsylvania, and Vermont. I show that variation in thresholds is considerable (Chapter II, III), as thresholds range from …

Wild Nyc: Building Biodiversity In Fresh Kills And City Parks, Melissa Zavala

Dissertations, Theses, and Capstone Projects

This dissertation is an anthropological field study of the work of urban ecological maintenance being conducted in New York City through the analysis of the reclamation and biotic restoration of the Fresh Kills landfill, located in the borough of Staten Island. This landfill was once the largest urban dump in the United States. Its 2,200 acres of trash buried in four mounds have polluted an area historically noted for its natural beauty as a collection of marshes and woodlands bordering the Kill Van Kull, a tidal strait that flows into the New York Harbor. The current plan for park and …

The Effect Of Population History On Hominoid Intraspecific Cranial Shape Diversity: Combining Population Genetic And 3d Geometric Morphometric Data, Julia Marie Zichello

Dissertations, Theses, and Capstone Projects

Cranial shape diversity within hominoids has been previously studied with the aim of understanding how levels of diversity in extant species compare with extinct hominin specimens. This dissertation addresses the question of why cranial shape diversity differs among extant hominoids. Levels of intraspecific cranial shape diversity are highly varied among hominoids. For example, Sumatran orangutan cranial shape diversity is more than twice that of all living humans. Here, the population history of each species, or sub-species, is considered as a force potentially structuring phenotypic variation. It is already well established that population history has shaped patterns of modern human cranial …

An Asian Origin Of Virulent Aeromonas Hydrophila Responsible For Disease Epidemics In United States-Farmed Catfish, Mohammad J. Hossain, Dawei Sun, Donald J. Mcgarey, Shannon Wrenn

Faculty Articles

Unlabelled: Since 2009, catfish farming in the southeastern United States has been severely impacted by a highly virulent and clonal population of Aeromonas hydrophila causing motile Aeromonas septicemia (MAS) in catfish. The possible origin of this newly emerged highly virulent A. hydrophila strain is unknown. In this study, we show using whole-genome sequencing and comparative genomics that A. hydrophila isolates from diseased grass carp in China and catfish in the United States have highly similar genomes. Our phylogenomic analyses suggest that U.S. catfish isolates emerged from A. hydrophila populations of Asian origin. Furthermore, we identified an A. hydrophila strain isolated …

The Economic Causes And Consequences Of Overweight And Obesity In The United States, David Alan Lempert

Dissertations, Theses, and Capstone Projects

Obesity is a serious public health issue, associated with increased risks of premature death, heart disease, diabetes, cancer, breathing problems, arthritis, reproductive complications, and other diseases. There are economic causes and consequences of overweight and obesity. Researchers have recently suggested that the inability of Body Mass Index to appropriately distinguish between body fat and non-body fat components may lead to inaccurate results when analyzing the economics of obesity. I use Percentage Body Fat, defined as Body Fat divided by the sum of Fat-Free Mass and Body Fat, as the primary measure of body composition.

A growing body of literature explores …

A Systematic Revision Of North American Tolypella A. Braun (Charophyceae, Charophyta), William Perez

Dissertations, Theses, and Capstone Projects

Charophyta comprises the algal classes Mesostigmatophyceae, Chlorokybophyceae, Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae and the land plants. However, the precise phylogenetic position of these algal classes with respect to land plants is unresolved as are the phylogenetic relationships among genera in Charophyceae (Characeae). Characeae contains two tribes with six genera: tribe Chareae (Chara, Lamprothamnium, Lychnothamnus and Nitellopsis) and tribe Nitelleae (Nitella and Tolypella). Tolypella was considered the third most species-rich genus but, in the most comprehensive taxonomic treatment of Characeae, 16 Tolypella species were consolidated into two species, T. nidifica and T. intricata in sections Rothia …

Computational Analyses Of The Components Of Sinorhizobium Meliloti Exor-Exos/Chvi Pathway: The Exor And Exos Proteins, Eliza M. Wiech

Dissertations, Theses, and Capstone Projects

The Sinorhizobium meliloti periplasmic ExoR protein and the ExoS/ChvI two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. In the absence of crystal structures, understanding the molecular mechanism of interaction between ExoR and the ExoS sensor, which is thought to drive the key regulatory step in the invasion process, remains a major challenge. In this study, we present theoretical structural models of the active form of ExoR protein, ExoRm, as well as of the sensing domain of ExoS, ExoSp, generated using computational methods. Our model suggests that ExoRm possesses a super-helical fold comprising …

Integration Or Interrogation? Franco-Maghrebi Rap And Hip-Hop Culture In Marseille, Jenna Catherine Daley

Dissertations, Theses, and Capstone Projects

This paper focuses on rap and hip-hop music that is produced from Franco-Maghrebi communities living in Marseille. The discussion revolves around the question of how rap music helps these communities to assimilate into French culture. The conclusion is two-fold. Marseille, as a city whose urban planning promotes physical assimilation of immigrants with French-born citizens, performs as an integrative force for these communities. Additionally, rap simultaneously assists Franco-Maghrebis in integrating into and subverting from French society. Franco-Maghrebi rappers integrate by becoming a part of mainstream French culture. Yet, they also subvert by extraordinarily placing race and discrimination at the forefront of …

Lgbtq Experiences With The Courts: The Role Of Gender Nonconformity And Assertiveness, Alexis Forbes

Dissertations, Theses, and Capstone Projects

Using lesbian, gay, bisexual, transgender, and queer (LGBTQ) and non-LGBTQ participants, a pair of studies explored the influence of LGBTQ identity and gender nonconformity (GNC) in experiences of discrimination in court settings. A one-way ANOVA tested whether LGBTQ participants were more likely to score low on the treatment in court scale. Additionally, two separate multiple regression analyses tested whether high scores on the Gender Nonconformity Scale (GNCS; Forbes & Nadal, under review), were associated with low scores on a measure of treatment in court. It was discovered that LGBTQ identity did not have a statistically significant effect on factor in …

Food, The Nutritional Product That Fuels The Passing Of Time: How Time And Nutrition Transformed Eating Into Refuelling, Diarmuid Cawley

Dublin Gastronomy Symposium

No abstract provided.

A Girl Power Study: Looking And Listening To The Role Of Emotions And Relationality In Developing Critical Consciousness, Jennifer Wallin-Ruschman

Dissertations and Theses

The concept of critical consciousness centers on the capacity for involvement in social change efforts. Its development has been the aim of many recent social movements (e.g., the consciousness raising groups of the women's movement). In this work, critical consciousness is defined as the highest level of socio-political-cultural (SPC) consciousness development. SPC consciousness is characterized by the linking of the personal and the political so that structures and discourses of oppression are not only understood but also lead to critical action and transforming relations of domination. Additionally, critical consciousness includes the ability to tolerate ambivalence and conflict as well as …

Pharmaceutical Risk Control Systems, Warren Adis

Communications of the IIMA

This paper outlines an initial investigation of the bio-pharmaceutical industry (BPI) and the steps it is taking to meet the new FDA risk mandate. It reviews the industry’s’ current strategy of improving its quality management systems that are central to achieving best practices within its operations. In addition the paper also reviews the strategy for upgrading to the next generation manufacturing execution systems which will control the enterprise facilities through full data integration and actionable intelligence.

4.419 Family And Medical Leave Policy

4.400 Hours of Work and Leave (Human Resources)

No abstract provided.

Cal Poly Biology Student Wins National Science Foundation Graduate Fellowship, Public Affairs Office

Press Releases

No abstract provided.

Targeted Maximum Likelihood Estimation Using Exponential Families, Iván Díaz, Michael Rosenblum

Johns Hopkins University, Dept. of Biostatistics Working Papers

Targeted maximum likelihood estimation (TMLE) is a general method for estimating parameters in semiparametric and nonparametric models. Each iteration of TMLE involves fitting a parametric submodel that targets the parameter of interest. We investigate the use of exponential families to define the parametric submodel. This implementation of TMLE gives a general approach for estimating any smooth parameter in the nonparametric model. A computational advantage of this approach is that each iteration of TMLE involves estimation of a parameter in an exponential family, which is a convex optimization problem for which software implementing reliable and computationally efficient methods exists. We illustrate …

Examining The Priorities Of The Canadian Chairmanship Of The Arctic Council: Current Obstacles In International Law, Policy, And Governance, Emma Barry-Pheby

Colorado Environmental Law Journal

No abstract provided.

Fine-Scale Features On The Sea Surface In Sar Satellite Imagery - Part 2: Numerical Modeling, Silvia Matt, A. Fujimura, Alexander Soloviev, S. H. Rhee, R. Romeiser

Marine & Environmental Sciences Faculty Articles

With the advent of the new generation of synthetic aperture radar (SAR) satellites, it has become possible to resolve fine-scale features on the sea surface on the scale of meters. The proper identification of sea surface signatures in SAR imagery can be challenging, since some features may be due to atmospheric distortions (gravity waves, squall lines) or anthropogenic influences (slicks), and may not be related to dynamic processes in the upper ocean. In order to improve our understanding of the nature of fine-scale features on the sea surface and their signature in SAR, we have conducted high-resolution numerical simulations combining …

Emotional Bias Of Cognitive Control In Adults With Childhood Attention-Deficit/Hyperactivity Disorder, Kurt P. Schulz, Anne-Claude V. Bédard, Jin Fan, Suzanne M. Clerkin, Danai Dima, Jeffrey H. Newcorn, Jeffrey M. Halperin

Publications and Research

Affect recognition deficits found in individuals with attention-deficit/hyperactivity disorder (ADHD) across the lifespan may bias the development of cognitive control processes implicated in the pathophysiology of the disorder. This study aimed to determine the mechanism through which facial expressions influence cognitive control in young adults diagnosed with ADHD in childhood. Fourteen probands with childhood ADHD and 14 comparison subjects with no history of ADHD were scanned with functional magnetic resonance imaging while performing a face emotion go/no-go task. Event-related analyses contrasted activation and functional connectivity for cognitive control collapsed over face valence and tested for variations in activation for response …

Oxidation Of Cellular Amino Acid Pools Leads To Cytotoxic Mistranslation Of The Genetic Code, Tammy J. Bullwinkle, Noah M. Reynolds, Medha Raina, Adil Moghal, Eleftheria Matsa, Andrei Rajkovic, Huseyin Kayadibi, Farbod Fazlollahi, Christopher Ryan, Nathaniel Howitz, Kym F. Faull, Beth A. Lazazzera, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aminoacyl-tRNA synthetases use a variety of mechanisms to ensure fidelity of the genetic code and ultimately select the correct amino acids to be used in protein synthesis. The physiological necessity of these quality control mechanisms in different environments remains unclear, as the cost vs benefit of accurate protein synthesis is difficult to predict. We show that in Escherichia coli, a non-coded amino acid produced through oxidative damage is a significant threat to the accuracy of protein synthesis and must be cleared by phenylalanine-tRNA synthetase in order to prevent cellular toxicity caused by mis-synthesized proteins. These findings demonstrate how stress …