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Pre-Whaling Genetic Diversity And Population Ecology In Eastern Pacific Gray Whales: Insights From Ancient Dna And Stable Isotopes, S Elizabeth Alter, Seth D. Newsome, Stephen R. Palumbi

Publications and Research

Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ,5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and …

The Conundrum Of Functional Brain Networks: Small-World Efficiency Or Fractal Modularity, Lazaros K. Gallos, Mariano Sigman, Hernán A. Makse

Publications and Research

The human brain has been studied at multiple scales, from neurons, circuits, areas with well-defined anatomical and functional boundaries, to large-scale functional networks which mediate coherent cognition. In a recent work, we addressed the problem of the hierarchical organization in the brain through network analysis. Our analysis identified functional brain modules of fractal structure that were inter-connected in a small-world topology. Here, we provide more details on the use of network science tools to elaborate on this behavior. We indicate the importance of using percolation theory to highlight the modular character of the functional brain network. These modules present a …

Interplay Of The Glass Transition And The Liquid-Liquid Phase Transition In Water, Nicolas Giovambattista, Thomas Loerting, Boris R. Lukanov, Francis W. Starr

Publications and Research

Water has multiple glassy states, often called amorphous ices. Low-density (LDA) and high-density (HDA) amorphous ice are separated by a dramatic, first-order like phase transition. It has been argued that the LDA-HDA transformation connects to a first-order liquid-liquid phase transition (LLPT) above the glass transition temperature Tg. Direct experimental evidence of the LLPT is challenging to obtain, since the LLPT occurs at conditions where water rapidly crystallizes. In this work, we explore the implications of a LLPT on the pressure dependence of Tg(P) for LDA and HDA by performing computer simulations of two water models – one with a LLPT, …

Cost Effective Malaria Risk Control Using Remote Sensing And Environmental Data, Md Zahidur Rahman, Leonid Roytman, Abdel Hamid Kadik

Publications and Research

Malaria transmission in many part of the world specifically in Bangladesh and southern African countries is unstable and epidemic. An estimate of over a million cases is reported annually. Malaria is heterogeneous, potentially due to variations in ecological settings, socio-economic status, land cover, and agricultural practices. Malaria control only relies on treatment and supply of bed networks. Drug resistance to these diseases is widespread. Vector control is minimal. Malaria control in those countries faces many formidable challenges such as inadequate accessibility to effective treatment, lack of trained manpower, inaccessibility of endemic areas, poverty, lack of education, poor health infrastructure and …

The Manufacture Of Lifestyle: The Role Of Corporations In Unhealthy Living, Nicholas Freudenberg

Publications and Research

Recently, researchers have debated two views on the connection between lifestyle and health. In the first, health-related lifestyles including tobacco and alcohol use, diet, and physical activity are seen as primary influences on health. In the second, social stratification is the dominant influence with lifestyles simply markers of social status. Neither approach leads to interventions that can reverse the world's most serious health problems. This article proposes that corporate practices are a dominant influence on the lifestyles that shape patterns of health and disease. Modifying business practices that promote unhealthy lifestyles is a promising strategy for improving population health. Corporations …

Twenty Years After: Armenian Research Libraries Today, D. Aram Donabedian, John Carey, Arshak Balayan

Publications and Research

Since achieving statehood in 1991, Armenia has faced major economic and political obstacles which have significantly affected the nation’s research libraries. This research paper will quantitatively and qualitatively examine the challenges facing Armenian research libraries just over twenty years after the collapse of the Soviet Union. Specifically, the authors analyze their interviews with five library administrators at five major institutions, respectively. These include Yerevan State University Library, the National Library of Armenia, the Fundamental Scientific Library of the National Academy of Sciences of Armenia, the Republican Scientific-Medical Library of Armenia, and the Papazian Library of the American University of Armenia. …

Accumulation And Rapid Decay Of Non-Ltr Retrotransposons In The Genome Of The Three-Spine Stickleback, Eryn Blass, Michael Bell, Stéphane Boissinot

Publications and Research

The diversity and abundance of non–long terminal repeat (LTR) retrotransposons (nLTR-RT) differ drastically among vertebrate genomes. At one extreme, the genome of placental mammals is littered with hundreds of thousands of copies resulting from the activity of a single clade of nLTR-RT, the L1 clade. In contrast, fish genomes contain a much more diverse repertoire of nLTR-RT, represented by numerous active clades and families. Yet, the number of nLTR-RT copies in teleostean fish is two orders of magnitude smaller than in mammals. The vast majority of insertions appear to be very recent, suggesting that nLTR-RT do not accumulate in fish …

Buddhist Hard Determinism: No Self, No Free Will, No Responsibility, Rick Repetti

Publications and Research

This is the third article in a four-article series that examines Buddhist responses to the Western philosophical problem of whether free will is compatible with “determinism,” the doctrine of universal causation. The first article (“Earlier”) focused on the first publications on this issue in the 1970s, the “early period.” The second (“Paleo-compatibilism”) and the present articles examine key responses published in the last part of the Twentieth and the first part of the Twenty-first centuries, the “middle period.” The fourth article (“Recent”) examines responses published in the last few years, the “recent period.” Whereas early-period scholars endorsed a compatibilism between …

Polyglutamine Toxicity Is Controlled By Prion Composition And Gene Dosage In Yeast, He Gong, Nina V. Romanova, Kim D. Allen, Pavithra Chandramowlishwaran, Kavita Gokhale, Gary P. Newnam, Piotr Miceczkowski, Michael Y. Sherman, Yury O. Chernoff

Publications and Research

Polyglutamine expansion causes diseases in humans and other mammals. One example is Huntington’s disease. Fragments of human huntingtin protein having an expanded polyglutamine stretch form aggregates and cause cytotoxicity in yeast cells bearing endogenous QN-rich proteins in the aggregated (prion) form. Attachment of the proline(P)-rich region targets polyglutamines to the large perinuclear deposit (aggresome). Aggresome formation ameliorates polyglutamine cytotoxicity in cells containing only the prion form of Rnq1 protein. Here we show that expanded polyglutamines both with (poly-QP) or without (poly-Q) a P-rich stretch remain toxic in the presence of the prion form of translation termination (release) factor Sup35 (eRF3). …

A Macroepigenetic Approach To Identify Factors Responsible For The Autism Epidemic In The United States, Renee Dufault, Walter J. Lukiw, Raquel Crider, Roseanne Schnoll, David Wallinga, Richard Deth

Publications and Research

The number of children ages 6 to 21 in the United States receiving special education services under the autism disability category increased 91% between 2005 to 2010 while the number of children receiving special education services overall declined by 5%. The demand for special education services continues to rise in disability categories associated with pervasive developmental disorders. Neurodevelopment can be adversely impacted when gene expression is altered by dietary transcription factors, such as zinc insufficiency or deficiency, or by exposure to toxic substances found in our environment, such as mercury or organophosphate pesticides. Gene expression patterns differ geographically between populations …

Life-Course Origins Of Social Inequalities In Adult Immune Cell Markers Of Inflammation In Developing Southern Chinese Population: The Guangzhou Biobank Cohort Study, Douglas A. West, Gabriel M. Leung, Chao Q. Jiang, Timothy M. Elwell-Sutton, Wei S. Zhang, Tai H. Lam, Kar K. Cheng, Mary Schooling

Publications and Research

Background
Socioeconomic position (SEP) throughout life is associated with cardiovascular disease, though the mechanisms linking these two are unclear. It is also unclear whether there are critical periods in the life course when exposure to better socioeconomic conditions confers advantages or whether SEP exposures accumulate across the whole life course. Inflammation may be a mechanism linking socioeconomic position (SEP) with cardiovascular disease. In a large sample of older residents of Guangzhou, in southern China, we examined the association of life course SEP with inflammation.

Methods
In baseline data on 9,981 adults (≥ 50 years old) from the Guangzhou Biobank Cohort …

Estimation Of Phosphorus Bioavailability In The Water Column Of The Bronx River, New York, Jingyu Wang, Hari K. Pant

Publications and Research

Phosphorus (P) is a primary limiting nutrient in rivers and streams, and excessive P results in eutrophication of freshwater systems, in turn, excessive algal growth/toxic algal blooms, oxygen depletion, and water quality degradation. This study analyzed P pool, and hydrolysis of organic P (OP) by native phosphatases (NPase) in the water samples collected in the Bronx River. The soluble reactive P (SRP) of most of the sites’ water collected in 2006 and 2007 were higher (average 67 µg·L–1 and 68 µg·L–1, respectively) than the US Environmental Protection Agency’s (EPA) standard of 15 µg·L–1. The SRP% (SRP/TP%) average was 27% in …

Brain Memoirs, Neuroscience, And The Self: A Review Article, Jason Tougaw

Publications and Research

No abstract provided.

Isolation And Biophysical Study Of Fruit Cuticles, Subhasish Chatterjee, Sayantani Sarkar, Julia Oktawiec, Zhantong Mao, Olivia Niitsoo, Ruth E. Stark

Publications and Research

The cuticle, a hydrophobic protective layer on the aerial parts of terrestrial plants, functions as a versatile defensive barrier to various biotic and abiotic stresses and also regulates water flow from the external environment.1 A biopolyester (cutin) and long-chain fatty acids (waxes) form the principal structural framework of the cuticle; the functional integrity of the cuticular layer depends on the outer 'epicuticular' layer as well as the blend consisting of the cutin biopolymer and 'intracuticular' waxes.2 Herein, we describe a comprehensive protocol to extract waxes exhaustively from commercial tomato (Solanum lycopersicum) fruit cuticles or to remove epicuticular and intracuticular waxes …

Nongenomic Mechanisms Of Pten Regulation, Jimmie E. Fata, Shawon Debnath, Edmund C. Jenkins, Marcia V. Fournier

Publications and Research

A large amount of data supports the view that PTEN is a bona fide tumor suppressor gene. However, recent evidence suggests that derailment of cellular localization and expression levels of functional nonmutated PTEN is a determining force in inducing abnormal cellular and tissue outcomes. As the cellular mechanisms that regulate normal PTEN enzymatic activity resolve, it is evident that deregulation of these mechanisms can alter cellular processes and tissue architecture and ultimately lead to oncogenic transformation. Here we discuss PTEN ubiquitination, PTEN complex formation with components of the adherens junction, PTEN nuclear localization, and microRNA regulation of PTEN as essential …

Integration Of Subthreshold And Suprathreshold Excitatory Barrages Along The Somatodendritic Axis Of Pyramidal Neurons, Hysell V. Oviedo, Alex D. Reyes

Publications and Research

Neurons integrate inputs arriving in different cellular compartments to produce action potentials that are transmitted to other neurons. Because of the voltage- and time-dependent conductances in the dendrites and soma, summation of synaptic inputs is complex. To examine summation of membrane potentials and firing rates, we performed whole-cell recordings from layer 5 cortical pyramidal neurons in acute slices of the rat’s somatosensory cortex. We delivered subthreshold and suprathreshold stimuli at the soma and several sites on the apical dendrite, and injected inputs that mimic synaptic barrages at individual or distributed sites. We found that summation of subthreshold potentials differed from …

Advances In Ultrafast Time Resolved Fluorescence Physics For Cancer Detection In Optical Biopsy, R. R. Alfano

Publications and Research

We discuss the use of time resolved fluorescence spectroscopy to extract fundamental kinetic information on molecular species in tissues. The temporal profiles reveal the lifetime and amplitudes associated with key active molecules distinguishing the local spectral environment of tissues. The femtosecond laser pulses at 310 nm excite the tissue. The emission profile at 340 nm from tryptophan is non-exponential due to the micro-environment. The slow and fast amplitudes and lifetimes of emission profiles reveal that cancer and normal states can be distinguished. Time resolved optical methods offer a new cancer diagnostic modality for the medical community.

Fellow Travellers: A Concordance Of Colonization Patterns Between Mice And Men In The North Atlantic Region, E P. Jones, K Skirnisson, T H. Mcgovern, Mtp Gilbert, E Willerslev, J B. Searle

Publications and Research

Background House mice (Mus musculus) are commensals of humans and therefore their phylogeography can reflect human colonization and settlement patterns. Previous studies have linked the distribution of house mouse mitochondrial (mt) DNA clades to areas formerly occupied by the Norwegian Vikings in Norway and the British Isles. Norwegian Viking activity also extended further westwards in the North Atlantic with the settlement of Iceland, short-lived colonies in Greenland and a fleeting colony in Newfoundland in 1000 AD. Here we investigate whether house mouse mtDNA sequences reflect human history in these other regions as well. Results House mice samples from Iceland, whether …

Sumoylation Is Tumor-Suppressive And Confers Proliferative Quiescence To Hematopoietic Progenitors In Drosophila Melanogaster Larvae, Marta E. Kalamarz, Indira Paddibhatla, Christina Nadar, Shubha Govind

Publications and Research

Summary How cell-intrinsic regulation of the cell cycle and the extrinsic influence of the niche converge to provide proliferative quiescence, safeguard tissue integrity, and provide avenues to stop stem cells from giving rise to tumors is a major challenge in gene therapy and tissue engineering. We explore this question in sumoylation-deficient mutants of Drosophila. In wild type third instar larval lymph glands, a group of hematopoietic stem/progenitor cells acquires quiescence; a multicellular niche supports their undifferentiated state. However, how proliferative quiescence is instilled in this population is not understood. We show that Ubc9 protein is nuclear in this population. Loss …

Using Equivalence-Based Instruction To Increase Efficiency In Teaching Neuroanatomy, Carolyn L. Pytte, Daniel M. Fienup

Publications and Research

A goal of all instruction is to efficiently allocate time spent teaching -- balancing redundancy that enhances learning with redundancy that is irrelevant to increasing student understanding. Efficient allocation of time allows the instructor to present additional material and go into more detail about the information being presented. Here we borrow laboratory research on concept formation and apply these formal principles in teaching introductory neuroanatomy within a lecture course on Behavioral Neuroscience. Concept formation is taught by pairing multiple stimuli, for instance brain name, location, and function, in such a way that novel associations within a category emerge without direct …

Genome Stability Of Lyme Disease Spirochetes: Comparative Genomics Of Borrelia Burgdorferi Plasmids, Sherwood R. Casjens, Emmanuel F. Mongodin, Wei-Gang Qiu, Benjamin J. Luft, Steven E. Schutzer, Eddie B. Gilcrease, Wai Mun Huang, Marija Vujadinovic, John K. Aron, Levy C. Vargas, Sam Freeman, Diana Radune, Janice F. Weidman, George I. Dimitrov, Hoda M. Khouri, Julia E. Sosa, Rebecca A. Halpin, John J. Dunn, Claire M. Fraser

Publications and Research

Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so are …

Entropy And The Complexity Of Graphs Revisited, Abbe Mowshowitz, Matthias Dehmer

Publications and Research

This paper presents a taxonomy and overview of approaches to the measurement of graph and network complexity. The taxonomy distinguishes between deterministic (e.g., Kolmogorov complexity) and probabilistic approaches with a view to placing entropy-based probabilistic measurement in context. Entropy-based measurement is the main focus of the paper. Relationships between the different entropy functions used to measure complexity are examined; and intrinsic (e.g., classical measures) and extrinsic (e.g., Körner entropy) variants of entropy-based models are discussed in some detail.

The Logic Of Fashion Cycles, Alberto Acerbi, Stefano Ghirlanda, Magnus Enquist

Publications and Research

Many cultural traits exhibit volatile dynamics, commonly dubbed fashions or fads. Here we show that realistic fashion-like dynamics emerge spontaneously if individuals can copy others' preferences for cultural traits as well as traits themselves. We demonstrate this dynamics in simple mathematical models of the diffusion, and subsequent abandonment, of a single cultural trait which individuals may or may not prefer. We then simulate the coevolution between many cultural traits and the associated preferences, reproducing power-law frequency distributions of cultural traits (most traits are adopted by few individuals for a short time, and very few by many for a long time), …

Queensborough Community College: Textbook Reserves, Sheila Beck

Publications and Research

This paper examines the textbook reserve collection at Queensborough Community College. Although the collection is heavily used in its current configuration, the library is looking for less labor intensive and less costly alternatives.

The cost of textbooks is skyrocketting. Textbooks are a major, unexpected bill for many students beginning college. Students and their family, used to having their textbooks provided or loaned free of charge at the start of the school year, face often large and unexpected bills when the first term begins. Many times, financial aid does not cover the cost of the books;. Even if it is covered …

Genetic Reporter System For Positioning Of Proteins At The Bacterial Pole, Kathryn R. Fixen, Anuradha Janakiraman, Sean Garritty, Daniel J. Slade, Andrew N. Gray, Nilay Karahan, Ann Hochschild, Marcia C. Goldberg

Publications and Research

Spatial organization within bacteria is fundamental to many cellular processes, although the basic mechanisms underlying localization of proteins to specific sites within bacteria are poorly understood. The study of protein positioning has been limited by a paucity of methods that allow rapid large-scale screening for mutants in which protein positioning is altered. We developed a genetic reporter system for protein localization to the pole within the bacterial cytoplasm that allows saturation screening for mutants in Escherichia coli in which protein localization is altered. Utilizing this system, we identify proteins required for proper positioning of the Shigella autotransporter IcsA. Autotransporters, widely …

Epidemiology And Management Of Depression Following Coronary Heart Disease Diagnosis In Women, Siqin Ye, Ellen-Ge Denton, Lauren T. Wasson, Karina W. Davidson

Publications and Research

Coronary heart disease (CHD) and depression are both highly prevalent in women. Importantly, depression is associated with significantly elevated morbidity and mortality in women with CHD. There are intriguing speculations about biological mechanisms underlying this association, such as endothelial dysfunction, subclinical atherosclerosis, inflammation, and autonomic dysregulation. Social and behavioral mechanisms, such as lack of social support and physical inactivity, have also been shown to play important roles. Unfortunately, many randomized clinical trials of counseling and pharmacologic interventions for depression in patients with CHD have failed to improve cardiovascular outcomes, and in fact have raised the possibility that interventions might be …

Independent Recruitment Of A Flavin-Dependent Monooxygenase For Safe Accumulation Of Sequestered Pyrrolizidine Alkaloids In Grasshoppers And Moths, Linzhu Wang, Till Beuerle, James Timbilla, Dietrich Ober

Publications and Research

Several insect lineages have developed diverse strategies to sequester toxic pyrrolizidine alkaloids from food-plants for their own defense. Here, we show that in two highly divergent insect taxa, the hemimetabolous grasshoppers and the holometabolous butterflies, an almost identical strategy evolved independently for safe accumulation of pyrrolizidine alkaloids. This strategy involves a pyrrolizidine alkaloid N-oxygenase that transfers the pyrrolizidine alkaloids to their respective N-oxide, enabling the insects to avoid high concentrations of toxic pyrrolizidine alkaloids in the hemolymph. We have identified a pyrrolizidine alkaloid N-oxygenase, which is a flavin-dependent monooxygenase, of the grasshopper Zonocerus variegatus. After heterologous expression in E. coli, …

Sendai Virus-Based Liposomes Enable Targeted Cytosolic Delivery Of Nanoparticles In Brain Tumor-Derived Cells, Veronica Dudu, Veronica Rotari, Maribel Vazquez

Publications and Research

BACKGROUND: Nanotechnology-based bioassays that detect the presence and/or absence of a combination of cell markers are increasingly used to identify stem or progenitor cells, assess cell heterogeneity, and evaluate tumor malignancy and/or chemoresistance. Delivery methods that enable nanoparticles to rapidly detect emerging, intracellular markers within cell clusters of biopsies will greatly aid in tumor characterization, analysis of functional state and development of treatment regimens.

RESULTS: Experiments utilized the Sendai virus to achieve in vitro, cytosolic delivery of Quantum dots in cells cultured from Human brain tumors. Using fluorescence microscopy and Transmission Electron Microscopy, in vitro experiments illustrated that these virus-based …

Coupling Of Fog And Marine Microbial Content In The Near-Shore Coastal Environment, M. E. Ducker, Gregory D. O'Mullan, K. C. Weathers, A. R. Juhl, M. Uriarte

Publications and Research

Microbes in the atmosphere (microbial aerosols) play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. However, the sources and environmental factors controlling the concentration, diversity, transport, and viability of microbial aerosols are poorly understood. This study examined culturable microbial aerosols from a coastal environment in Maine (USA) and determined the effect of onshore wind speed and fog presence on deposition rate, source, and community composition. During fog events with low onshore winds (

Genetic Signatures Of A Demographic Collapse In A Large-Bodied Forest Dwelling Primate (Mandrillus Leucophaeus), Nelson Ting, Christos Astaras, Gail Hearn, Shaya Honarvar, Joel Corush, Andrew S. Burrell, Naomi Phillips, Bethan J. Morgan, Elizabeth L. Gadsby, Ryan L. Raaum, Christian Roos

Publications and Research

It is difficult to predict how current climate change will affect wildlife species adapted to a tropical rainforest environment. Understanding how population dynamics fluctuated in such species throughout periods of past climatic change can provide insight into this issue. The drill (Mandrillus leucophaeus) is a large-bodied rainforest adapted mammal found in West Central Africa. In the middle of this endangered monkey’s geographic range is Lake Barombi Mbo, which has a well-documented palynological record of environmental change that dates to the Late Pleistocene. We used a Bayesian coalescent-based framework to analyze 2,076 base pairs of mitochondrial DNA across wild drill populations …