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RESEARCH QUESTION: Does Online "Working Out Work" as a Treatment and Prevention for Depression in Older Adults? An Analysis of a Prescribed and Monitored Exercise Program Administered via the Internet for Senior Adults with Depression.
OBJECTIVE: The purpose of this study is to investigate and access the effectiveness of an online

RESEARCH QUESTION: Does Online "Working Out Work" as a Treatment and Prevention for Depression in Older Adults? An Analysis of a Prescribed and Monitored Exercise Program Administered via the Internet for Senior Adults with Depression.
OBJECTIVE: The purpose of this study is to investigate and access the effectiveness of an online prescribed and monitored exercise program for the treatment of depression in Older Adults. The Dependent Variable for the study is Depression. The Independent Variable for the study is the Effects of Exercise administered via the Internet and the population is geriatric adults defined as senior adults aged 50 and older. Depression is defined by Princeton University Scholars (Wordnet, 2006) as a mental state characterized by a pessimistic sense of inadequacy and a despondent lack of activity.
METHODS: The presence and severity of depression will be assessed by using The Merck Manual of Geriatrics (GDS-15) Geriatric Depression Scale. Assessments will be performed at baseline, before and after the treatment is concluded. The subjects will complete the Physical Activity Readiness Questionnaire (PAR-Q) prior to participating in an exercise program three times per week.
LIMITATIONS OF RESEARCH: The limitations of this study are: 1) There is a small sample size limited to Senior Adults aged 50 - 80, and 2) there is no control group with structured activity or placebo, therefore researcher is unable to evaluate if the marked improvement was due to a non-specific therapeutic effect associated with taking part in a social activity (group online exercise program). Further research could compare and analyze the positive effects of a muscular strength training exercise program verses a cardiovascular training exercise program.

ContributorsCaballero-Garcia, Robelyn (Author) / Waldron, Kathleen (Thesis advisor) / College of Liberal Arts and Sciences (Contributor)
Created2011-05-02
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Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a

Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic). The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P) regimes (P only, N:P = 16 and N:P = 75 by atoms). In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.

ContributorsLee, Zarraz (Author) / Poret-Peterson, Amisha (Author) / Siefert, Janet L. (Author) / Kaul, Drishti (Author) / Moustafa, Ahmed (Author) / Allen, Andrew E. (Author) / Dupont, Chris L. (Author) / Eguiarte, Luis E. (Author) / Souza, Valeria (Author) / Elser, James (Author) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / School of Earth and Space Exploration (Contributor)
Created2017-05-30
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I present the case for a fire-centric scholarship, and suggest the transition between burning living landscapes and lithic ones (in the form of fossil fuels) would make a good demonstration of what such scholarship might do and what its value could be.

ContributorsPyne, Stephen (Author) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2017-10-23
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Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum

Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electron laser sources.
ContributorsAquila, A. (Author) / Barty, A. (Author) / Bostedt, C. (Author) / Boutet, S. (Author) / Carini, G. (Author) / dePonte, D. (Author) / Drell, P. (Author) / Doniach, S. (Author) / Downing, K. H. (Author) / Earnest, T. (Author) / Elmlund, H. (Author) / Elser, V. (Author) / Guhr, M. (Author) / Hajdu, J. (Author) / Hastings, J. (Author) / Hau-Riege, S. P. (Author) / Huang, Z. (Author) / Lattman, E. E. (Author) / Maia, F. R. N. C. (Author) / Marchesini, S. (Author) / Ourmazd, A. (Author) / Pellegrini, C. (Author) / Santra, R. (Author) / Schlichting, I. (Author) / Schroer, C. (Author) / Spence, John (Author) / Vartanyants, I. A. (Author) / Wakatsuki, S. (Author) / Weis, W. I. (Author) / Williams, G. J. (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2015-04-21
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The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity,

The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10–100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also permit an analysis of the dependence of crystal quality on crystal size.
ContributorsAbdallah, Bahige (Author) / Zatsepin, Nadia (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Conrad, Chelsie (Author) / Dorner, Katerina (Author) / Sierra, Raymond G. (Author) / Stevenson, Hilary P. (Author) / Camacho Alanis, Fernanda (Author) / Grant, Thomas D. (Author) / Nelson, Garrett (Author) / James, Daniel (Author) / Calero, Guillermo (Author) / Wachter, Rebekka (Author) / Spence, John (Author) / Weierstall, Uwe (Author) / Fromme, Petra (Author) / Ros, Alexandra (Author) / Department of Chemistry and Biochemistry (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-08-19
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Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after

Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes. In order to investigate these hypotheses we estimated the evolutionary ages of all human genes and then studied the probability of mutation and their biological function in relation to their age and genomic location for both normal germline and cancer contexts.

We observed that under a model of uniform random mutation across the genome, controlled for gene size, genes less than 500 MY were more frequently mutated in both cases. Paradoxically, causal genes, defined in the COSMIC Cancer Gene Census, were depleted in this age group. When we used functional enrichment analysis to explain this unexpected result we discovered that COSMIC genes with recessive disease phenotypes were enriched for DNA repair and cell cycle control. The non-mutated genes in these pathways are orthologous to those underlying stress-induced mutation in bacteria, which results in the clustering of single nucleotide variations. COSMIC genes were less common in regions where the probability of observing mutational clusters is high, although they are approximately 2-fold more likely to harbor mutational clusters compared to other human genes. Our results suggest this ancient mutational response to stress that evolved among prokaryotes was co-opted to maintain diversity in the germline and immune system, while the original phenotype is restored in cancer. Reversion to a stress-induced mutational response is a hallmark of cancer that allows for effectively searching “protected” genome space where genes causally implicated in cancer are located and underlies the high adaptive potential and concomitant therapeutic resistance that is characteristic of cancer.

Created2017-04-25
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Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory,

Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an isolated system, and innovation as trajectories not observed in isolated systems. As a case study, we implement novel variants of cellular automata (CA) where the update rules are allowed to vary with time in three alternative ways. Each is capable of generating conditions for open-ended evolution, but vary in their ability to do so. We find that state-dependent dynamics, regarded as a hallmark of life, statistically out-performs other candidate mechanisms, and is the only mechanism to produce open-ended evolution in a scalable manner, essential to the notion of ongoing evolution. This analysis suggests a new framework for unifying mechanisms for generating OEE with features distinctive to life and its artifacts, with broad applicability to biological and artificial systems.
Created2017-04-20
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Toward the end of his career, Zewail developed strong interest in fast electron spectroscopy and imaging, a field to which he made important contributions toward his aim of making molecular movies free of radiation damage. We therefore compare here the atomistic mechanisms leading to destruction of protein samples in diffract-and-destroy

Toward the end of his career, Zewail developed strong interest in fast electron spectroscopy and imaging, a field to which he made important contributions toward his aim of making molecular movies free of radiation damage. We therefore compare here the atomistic mechanisms leading to destruction of protein samples in diffract-and-destroy experiments for the cases of high-energy electron beam irradiation and X-ray laser pulses. The damage processes and their time-scales are compared and relevant elastic, inelastic, and photoelectron cross sections are given. Inelastic mean-free paths for ejected electrons at very low energies in insulators are compared with the bioparticle size. The dose rate and structural damage rate for electrons are found to be much lower, allowing longer pulses, reduced beam current, and Coulomb interactions for the formation of smaller probes. High-angle electron scattering from the nucleus, which has no parallel in the X-ray case, tracks the slowly moving nuclei during the explosion, just as the gain of the XFEL (X-ray free-electron laser) has no parallel in the electron case. Despite reduced damage and much larger elastic scattering cross sections in the electron case, leading to not dissimilar elastic scattering rates (when account is taken of the greatly increased incident XFEL fluence), progress for single-particle electron diffraction is seen to depend on the effort to reduce emittance growth due to Coulomb interactions, and so allow formation of intense sub-micron beams no larger than a virus.
ContributorsSpence, John (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2017-06-01
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pH and fermentable substrates impose selective pressures on gut microbial communities and their metabolisms. We evaluated the relative contributions of pH, alkalinity, and substrate on microbial community structure, metabolism, and functional interactions using triplicate batch cultures started from fecal slurry and incubated with an initial pH of 6.0, 6.5, or

pH and fermentable substrates impose selective pressures on gut microbial communities and their metabolisms. We evaluated the relative contributions of pH, alkalinity, and substrate on microbial community structure, metabolism, and functional interactions using triplicate batch cultures started from fecal slurry and incubated with an initial pH of 6.0, 6.5, or 6.9 and 10 mM glucose, fructose, or cellobiose as the carbon substrate. We analyzed 16S rRNA gene sequences and fermentation products. Microbial diversity was driven by both pH and substrate type. Due to insufficient alkalinity, a drop in pH from 6.0 to ~4.5 clustered pH 6.0 cultures together and distant from pH 6.5 and 6.9 cultures, which experienced only small pH drops. Cellobiose yielded more acidity than alkalinity due to the amount of fermentable carbon, which moved cellobiose pH 6.5 cultures away from other pH 6.5 cultures. The impact of pH on microbial community structure was reflected by fermentative metabolism. Lactate accumulation occurred in pH 6.0 cultures, whereas propionate and acetate accumulations were observed in pH 6.5 and 6.9 cultures and independently from the type of substrate provided. Finally, pH had an impact on the interactions between lactate-producing and -consuming communities. Lactate-producing Streptococcus dominated pH 6.0 cultures, and acetate- and propionate-producing Veillonella, Bacteroides, and Escherichia dominated the cultures started at pH 6.5 and 6.9. Acid inhibition on lactate-consuming species led to lactate accumulation. Our results provide insights into pH-derived changes in fermenting microbiota and metabolisms in the human gut.
Created2017-05-03
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Cataclysmic Variables (CVs) are close binary star systems with one component a white dwarf (WD) and the other a larger cooler star that fills its Roche Lobe. The cooler star is losing mass through the inner Lagrangian point of the binary and some unknown fraction of this material is accreted

Cataclysmic Variables (CVs) are close binary star systems with one component a white dwarf (WD) and the other a larger cooler star that fills its Roche Lobe. The cooler star is losing mass through the inner Lagrangian point of the binary and some unknown fraction of this material is accreted by the WD. One consequence of the WDs accreting material, is the possibility that they are growing in mass and will eventually reach the Chandrasekhar Limit. This evolution could result in a Supernova Ia (SN Ia) explosion and is designated the Single Degenerate Progenitor (SD) scenario. This paper is concerned with the SD scenario for SN Ia progenitors. One problem with the single degenerate scenario is that it is generally assumed that the accreting material mixes with WD core material at some time during the accretion phase of evolution and, since the typical WD has a carbon-oxygen CO core, the mixing results in large amounts of carbon and oxygen being brought up into the accreted layers. The presence of enriched carbon causes enhanced nuclear fusion and a Classical Nova explosion.

Both observations and theoretical studies of these explosions imply that more mass is ejected than is accreted. Thus, the WD in a Classical Nova system is losing mass and cannot be a SN Ia progenitor. However, the composition in the nuclear burning region is important and, in new calculations reported here, the consequences to the WD of no mixing of accreted material with core material have been investigated so that the material involved in the explosion has only a Solar composition. WDs with a large range in initial masses and mass accretion rates have been evolved. I find that once sufficient material has been accreted, nuclear burning occurs in all evolutionary sequences and continues until a thermonuclear runaway (TNR) occurs and the WD either ejects a small amount of material or its radius grows to about 10[superscript 12] cm and the evolution is ended. In all cases where mass ejection occurs, the mass of the ejecta is far less than the mass of the accreted material. Therefore, all the WDs are growing in mass. It is also found that the accretion time to explosion can be sufficiently short for a 1.0M[subscript ⊙] WD that recurrent novae can occur on a low mass WD. This mass is lower than typically assumed for the WDs in recurrent nova systems. Finally, the predicted surface temperatures when the WD is near the peak of the explosion imply that only the most massive WDs will be significant X-ray emitters at this time.

Created2014-02-25