Showing 1471 - 1480 of 2039 Items
Correcting in situ chlorophyll fluorescence time-series observations for nonphotochemical quenching and tidal variability reveals nonconservative phytoplankton variability in coastal waters
Date: 2019-08-01
Creator: Luke Carberry
Collin Roesler
Susan Drapeau
Access: Open access
- Chlorophyll fluorometry is one of the most commonly implemented approaches for estimating phytoplankton biomass in situ, despite documented sources of natural variability and instrumental uncertainty in the relationship between in vivo fluorescence and chlorophyll concentration. A number of strategies are employed to minimize errors and quantify natural variability in this relationship in the open ocean. However, the assumptions underlying these approaches are unsupported in coastal waters due to the short temporal and small spatial scales of variability, as well as the optical complexity. The largest source of variability in the in situ chlorophyll fluorometric signal is nonphotochemical quenching (NPQ). Typically, unquenched nighttime observations are interpolated over the quenched daytime interval, but this assumes a spatial homogeneity not found in tidally impacted coastal waters. Here, we present a model that provides a tidally resolved correction for NPQ in moored chlorophyll fluorescence measurements. The output of the model is a time series of unquenched chlorophyll fluorescence in tidal endmembers (high and low tide extremes), and thus a time series of phytoplankton biomass growth and loss in these endmember populations. Comparison between modeled and measured unquenched time series yields quantification of nonconservative variations in phytoplankton biomass. Tidally modeled interpolation between these endmember time series yields a highly resolved time series of unquenched daytime chlorophyll fluorescence values at the location of the moored sensor. Such data sets provide a critical opportunity for validating the satellite remotely sensed ocean color chlorophyll concentration data product in coastal waters.
An architecture for emotional decision-making agents
Date: 2002-01-01
Creator: Eric Chown
Randolph M. Jones
Amy E. Henninger
Access: Open access
- Our research focuses on complex agents that are capable of interacting with their environments in ways that are increasingly similar to individual humans. In this article we describe a cognitive architecture for an interactive decision-making agent with emotions. The primary goal of this work is to make the decision-making process of complex agents more realistic with regard to the behavior moderators, including emotional factors that affect humans. Instead of uniform agents that rely entirely on a deterministic body of expertise to make their decisions, the decision making process of our agents will vary according to select emotional factors affecting the agent as well as the agent's parameterized emotional profile. The premise of this model is that emotions serve as a kind of automatic assessment system that can guide or otherwise influence the more deliberative decision making process. The primary components of this emotional system are pleasure/pain and clarity/confusion subsystems that differentiate between positive and negative states. These, in turn, feed into an arousal system that interfaces with the decision-making system. We are testing our model using synthetic special-forces agents in a reconnaissance simulation.
Transgenic analysis of Dlx regulation in fish tooth development reveals evolutionary retention of enhancer function despite organ loss
Date: 2006-12-19
Creator: William R. Jackman
David W. Stock
Access: Open access
- It has been considered a "law" that a lost structure cannot reappear in evolution. The common explanation, that genes required for the development of the lost structure degrade by mutation, remains largely theoretical, however. Additionally, the extent to which this mechanism applies to systems of repeated parts, where individual modules are likely to exhibit few unique aspects of genetic control, is unclear. We investigated reversibility of evolution in one such system, the vertebrate dentition, using as a model loss of oral teeth in cypriniform fishes, which include the zebra fish. This evolutionary event, which occurred >50 million years ago, has not been reversed despite subsequent diversification of feeding modes and retention of pharyngeal teeth. We asked whether the cis-regulatory region of a gene whose expression loss parallels cypriniform tooth loss, Dlx2b, retains the capacity for expression in oral teeth. We first created a zebrafish reporter transgenic line that recapitulates endogenous dlx2b expression. We then showed that this zebrafish construct drives reporter expression in oral teeth of the related characiform Astyanax mexicanus. This result, along with our finding that Dlx genes are required for normal tooth development, suggests that changes in trans-acting regulators of these genes were responsible for loss of cypriniform oral teeth. Preservation of oral enhancer function unused for >50 million years could be the result of pleiotropic function in the pharyngeal dentition. If enhancers of other genes in the tooth developmental pathway are similarly preserved, teeth lost from specific regions may be relatively easy to reacquire in evolution. © 2006 by The National Academy of Sciences of the USA.
Developmental genetic mechanisms of evolutionary tooth loss in cypriniform fishes
Date: 2006-08-01
Creator: David W. Stock
William R. Jackman
Josh Trapani
Access: Open access
- The fossil record indicates that cypriniform fishes, a group including the zebrafish, lost oral teeth over 50 million years ago. Despite subsequent diversification of feeding modes, no cypriniform has regained oral teeth, suggesting the zebrafish as a model for studying the developmental genetic basis of evolutionary constraint. To investigate the mechanism of cypriniform tooth loss, we compared the oral expression of seven genes whose mammalian orthologs are involved in tooth initiation in the zebrafish and the Mexican tetra, Astyanax mexicanus, a related species retaining oral teeth. The most significant difference we found was an absence in zebrafish oral epithelium of expression of dlx2a and dlx2b, transcription factors that are expressed in early Astyanax odontogenic epithelium. Analysis of orthologous genes in the Japanese medaka (Oryzias latipes) and a catfish (Synodontis multipunctatus) suggests that expression was lost in cypriniforms, rather than gained in Astyanax. Treatment of Astyanaxwith an inhibitor of Fibroblast growth factor (Fgf) signaling produced a partial phenocopy of the zebrafish oral region, in that oral teeth, and expression of d1x2a and d1x2b, were lost, whereas shh and pitx2, genes whose expression is present in zebrafish oral epithelium, were unaffected. We hypothesize that a loss of Fgf signaling to oral epithelium was associated with cypriniform tooth loss.
Discrete breathers in a mass-in-mass chain with Hertzian local resonators
Date: 2017-02-22
Creator: S. P. Wallen
J. Lee
D. Mei
C. Chong
P. G., Kevrekidis
N. Boechler
Access: Open access
- We report on the existence of discrete breathers in a one-dimensional, mass-in-mass chain with linear intersite coupling and nonlinear, precompressed Hertzian local resonators, which is motivated by recent studies of the dynamics of microspheres adhered to elastic substrates. After predicting theoretically the existence of discrete breathers in the continuum and anticontinuum limits of intersite coupling, we use numerical continuation to compute a family of breathers interpolating between the two regimes in a finite chain, where the displacement profiles of the breathers are localized around one lattice site. We then analyze the frequency-amplitude dependence of the breathers by performing numerical continuation on a linear eigenmode (vanishing amplitude) solution of the system near the upper band gap edge. Finally, we use direct numerical integration of the equations of motion to demonstrate the formation and evolution of the identified localized modes in energy-conserving and dissipative scenarios, including within settings that may be relevant to future experimental studies.
The Importance of What We Care About: A Solidarity Approach to Resource Allocation
Date: 2020-01-01
Creator: Kristi A. Olson
Access: Open access
- At some point in your life, you will need to allocate resources among individuals, but how should you do so? One prominent suggestion is the envy test: the envy test is satisfied when and only when no one prefers someone else’s bundle. In Part I, I explain and then reject Tom Parr’s recent attempt to justify the envy test. Yet, like Parr, I believe the envy test captures something important. Thus, in Part II, I distinguish two approaches to resource allocation. Parr’s defense of the envy test assumes what I will call an individualist approach: what matters are each individual’s preferences. In lieu of the individualist approach, I endorse the solidarity approach: what matters are everyone’s preferences. After explaining the distinction, I show that the envy test—or at least something like it—can be defended using the solidarity approach even if it cannot be defended using the individualist approach.
Anthropogenic Impacts on Atmospheric Carbonyl Sulfide Since the 19th Century Inferred From Polar Firn Air and Ice Core Measurements
Date: 2020-08-27
Creator: M. Aydin
G. L. Britten
S. A. Montzka
C. Buizert
F., Primeau
V. Petrenko
M. B. Battle
M. R. Nicewonger
J. Patterson
B. Hmiel
E. S. Saltzman
Access: Open access
- Carbonyl sulfide (COS) was measured in firn air collected during seven different field campaigns carried out at four different sites in Greenland and Antarctica between 2001 and 2015. A Bayesian probabilistic statistical model is used to conduct multisite inversions and to reconstruct separate atmospheric histories for Greenland and Antarctica. The firn air inversions cover most of the 20th century over Greenland and extend back to the 19th century over Antarctica. The derived atmospheric histories are consistent with independent surface air time series data from the corresponding sites and the Antarctic ice core COS records during periods of overlap. Atmospheric COS levels began to increase over preindustrial levels starting in the 19th century, and the increase continued for much of the 20th century. Atmospheric COS peaked at higher than present-day levels around 1975 CE over Greenland and around 1987 CE over Antarctica. An atmosphere/surface ocean box model is used to investigate the possible causes of observed variability. The results suggest that changes in the magnitude and location of anthropogenic sources have had a strong influence on the observed atmospheric COS variability.
Formation of rarefaction waves in origami-based metamaterials
Date: 2016-04-15
Creator: H. Yasuda
C. Chong
E. G. Charalampidis
P. G. Kevrekidis
J., Yang
Access: Open access
- We investigate the nonlinear wave dynamics of origami-based metamaterials composed of Tachi-Miura polyhedron (TMP) unit cells. These cells exhibit strain softening behavior under compression, which can be tuned by modifying their geometrical configurations or initial folded conditions. We assemble these TMP cells into a cluster of origami-based metamaterials, and we theoretically model and numerically analyze their wave transmission mechanism under external impact. Numerical simulations show that origami-based metamaterials can provide a prototypical platform for the formation of nonlinear coherent structures in the form of rarefaction waves, which feature a tensile wavefront upon the application of compression to the system. We also demonstrate the existence of numerically exact traveling rarefaction waves in an effective lumped-mass model. Origami-based metamaterials can be highly useful for mitigating shock waves, potentially enabling a wide variety of engineering applications.
Captured segment exchange: A strategy for custom engineering large genomic regions in Drosophila melanogaster
Date: 2013-04-24
Creator: Jack R. Bateman
Michael F. Palopoli
Sarah T. Dale
Jennifer E. Stauffer
Anita L., Shah
Justine E. Johnson
Conor W. Walsh
Hanna Flaten
Christine M. Parsons
Access: Open access
- Site-specific recombinases (SSRs) are valuable tools for manipulating genomes. In Drosophila, thousands of transgenic insertions carrying SSR recognition sites have been distributed throughout the genome by several large-scale projects. Here we describe a method with the potential to use these insertions to make custom alterations to the Drosophila genome in vivo. Specifically, by employing recombineering techniques and a dual recombinase-mediated cassette exchange strategy based on the phiC31 integrase and FLP recombinase, we show that a large genomic segment that lies between two SSR recognition-site insertions can be "captured" as a target cassette and exchanged for a sequence that was engineered in bacterial cells. We demonstrate this approach by targeting a 50-kb segment spanning the tsh gene, replacing the existing segment with corresponding recombineered sequences through simple and efficient manipulations. Given the high density of SSR recognition-site insertions in Drosophila, our method affords a straightforward and highly efficient approach to explore gene function in situ for a substantial portion of the Drosophila genome. © 2013 by the Genetics Society of America.
Efficient and rapid identification of Candida albicans allelic status using SNP-RFLP
Date: 2009-11-01
Creator: Anja Forche
Musetta Steinbach
Judith Berman
Access: Open access
- Candida albicans is the most prevalent opportunistic fungal pathogen in the clinical setting, causing a wide spectrum of diseases ranging from superficial mucosal lesions to life-threatening deep-tissue infections. Recent studies provide strong evidence that C. albicans possesses an arsenal of genetic mechanisms promoting genome plasticity and that it uses these mechanisms under conditions of nutritional or antifungal drug stress. Two microarray-based methods, single nucleotide polymorphism (SNP) and comparative genome hybridization arrays, have been developed to study genome changes in C. albicans. However, array technologies can be relatively expensive and are not available to every laboratory. In addition, they often generate more data than needed to analyze specific genomic loci or regions. Here, we have developed a set of SNP-restriction fragment length polymorphism (RFLP) (or PCR-RFLP) markers, two per chromosome arm, for C. albicans. These markers can be used to rapidly and accurately detect large-scale changes in the C. albicans genome including loss of heterozygosity (LOH) at single loci, across chromosome arms or across whole chromosomes. Furthermore, skewed SNP-RFLP allelic ratios are indicative of trisomy at heterozygous loci. While less comprehensive than array-based approaches, we propose SNP-RFLP as an inexpensive, rapid, and reliable method to screen strains of interest for possible genome changes. © 2009 Federation of European Microbiological Societies.