Showing 1991 - 2000 of 2040 Items
Quantitative estimation of localization errors of 3 d transition metal pseudopotentials in diffusion Monte Carlo
Date: 2017-07-14
Creator: Allison L. Dzubak
Jaron T. Krogel
Fernando A. Reboredo
Access: Open access
- The necessarily approximate evaluation of non-local pseudopotentials in diffusion Monte Carlo (DMC) introduces localization errors. We estimate these errors for two families of non-local pseudopotentials for the first-row transition metal atoms Sc-Zn using an extrapolation scheme and multideterminant wavefunctions. Sensitivities of the error in the DMC energies to the Jastrow factor are used to estimate the quality of two sets of pseudopotentials with respect to locality error reduction. The locality approximation and T-moves scheme are also compared for accuracy of total energies. After estimating the removal of the locality and T-moves errors, we present the range of fixed-node energies between a single determinant description and a full valence multideterminant complete active space expansion. The results for these pseudopotentials agree with previous findings that the locality approximation is less sensitive to changes in the Jastrow than T-moves yielding more accurate total energies, however not necessarily more accurate energy differences. For both the locality approximation and T-moves, we find decreasing Jastrow sensitivity moving left to right across the series Sc-Zn. The recently generated pseudopotentials of Krogel et al. [Phys. Rev. B 93, 075143 (2016)] reduce the magnitude of the locality error compared with the pseudopotentials of Burkatzki et al. [J. Chem. Phys. 129, 164115 (2008)] by an average estimated 40% using the locality approximation. The estimated locality error is equivalent for both sets of pseudopotentials when T-moves is used. For the Sc-Zn atomic series with these pseudopotentials, and using up to three-body Jastrow factors, our results suggest that the fixed-node error is dominant over the locality error when a single determinant is used.
Reviews fall 2019-Special issue on Bauhaus centenary
Date: 2019-01-01
Creator: Kathleen James-Chakraborty
Pep Avilés
Claudia Tittel
Jill Pearlman
Access: Open access
Receptors and Neuropeptides in the Cardiac Ganglion of the American Lobster, Homarus americanus: A Bioinformatics and Mass Spectrometric Investigation
Date: 2019-01-01
Creator: Louis Mendez
Access: Open access
- Central pattern generators (CPGs) are neural networks that generate rhythmic motor patterns to allow organisms to perform stereotypical tasks, such as breathing, scratching, flying, and walking. The American lobster, Homarus americanus, is a simple model system whose CPGs are functionally analogous to those in vertebrate models and model complex rhythmic behaviors. CPGs in many Crustacea, including the American lobster, have been studied because of their ability to maintain biological function after isolation in physiologically relevant conditions. The cardiac ganglion (CG) is a CPG consisting of five larger motor neurons and four smaller pacemaker neurons that innervate the cardiac neuromuscular system and generate electrical bursts that drive patterned behaviors. Neuromodulators, such as neuropeptides, are known to modulate neural output in the CPGs of the American lobster. Currently, neuromodulators affecting the cardiac ganglia are thought to be mainly expressed and secreted outside of the cardiac ganglia, acting as extrinsic neuromodulators. However, there is current evidence to support the idea that neuromodulators can be intrinsically expressed within the cardiac ganglion of the American lobster. Preliminary studies using transcriptomic techniques on genomic and transcriptomic information indicate that neuropeptides are likely expressed within the cardiac ganglion. However, little research has been done to determine whether these neuropeptides are expressed in the cardiac ganglion of the American lobster. Therefore, the purpose of this study is to combine bioinformatics and mass spectrometric techniques to determine whether select neuropeptides are present in the cardiac ganglion within the cardiac neuromuscular system of the American lobster, Homarus americanus. Our data mining techniques using protein query sequences obtained from previously annotated brain and eyestalk transcriptomes resulted in the identification of 22 putative neuropeptides preprohormones from 17 neuropeptide families and 20 putative neuropeptide receptors from 17 neuropeptide receptor families in the CG transcriptome. Additionally, 9 putative neuropeptide receptors from 7 neuropeptide receptor families were detected in the cardiac muscle transcriptome. Of the 17 neuropeptide families detected, receptors for 9 of these neuropeptide families were detected in the CG transcriptome. Receptors for 6 of the neuropeptide families were also present in the cardiac muscle transcriptome. Interestingly, receptors for 6 of neuropeptide families detected were not found in either the CG or cardiac muscle transcriptomes, and receptors for 4 neuropeptide families that weren’t detected in the CG transcriptome were found in the cardiac muscle transcriptome. Therefore, our research suggests that neuropeptides are able to modulate CPG activity extrinsically, either though hormonal or local delivery, or intrinsically. Additionally, neuropeptides were extracted from the stomatogastric ganglion and the commissural ganglion using a scaled-down neuropeptide extraction protocol to estimate the number of tissues required to obtain sufficiently strong mass spectrometry signals. Pooled samples with two commissural ganglia and single samples of a commissural ganglion and a stomatogastric ganglion displayed little signal and an increase in larger peptides and impurities relative to single-tissue samples. Therefore, further optimization of the scaled-down neuropeptide extraction protocol must be done prior to analysis of a cardiac ganglion in the American lobster.
Sensory-based niche partitioning in a multiple predator-multiple prey community
Date: 2015-05-20
Creator: Jay J. Falk
Hannah M. Ter Hofstede
Patricia L. Jones
Marjorie M. Dixon
Paul A., Faure
Elisabeth K.V. Kalko
Rachel A. Page
Access: Open access
- Many predators and parasites eavesdrop on the communication signals of their prey. Eavesdropping is typically studied as dyadic predator-prey species interactions; yet in nature, most predators target multiple prey species and most prey must evade multiple predator species. The impact of predator communities on prey signal evolution is not well understood. Predators could converge in their preferences for conspicuous signal properties, generating competition among predators and natural selection on particular prey signal features. Alternatively, predator species could vary in their preferences for prey signal properties, resulting in sensory-based niche partitioning of prey resources. In the Neotropics, many substrate-gleaning bats use the mate-attraction songs of male katydids to locate them as prey. We studied mechanisms of niche partitioning in four substrate- gleaning bat species and found they are similar in morphology, echolocation signal design and prey-handling ability, but each species preferred different acoustic features of male song in 12 sympatric katydid species. This divergence in predator preference probably contributes to the coexistence of many substrate-gleaning bat species in the Neotropics, and the substantial diversity in the mate-attraction signals of katydids. Our results provide insight into how multiple eavesdropping predator species might influence prey signal evolution through sensory-based niche partitioning.
When to approach novel prey cues? Social learning strategies in frog-eating bats
Date: 2013-10-23
Creator: Patricia L. Jones
Michael J. Ryan
Victoria Flores
Rachel A. Page
Access: Open access
- Animals can use different sources of information when making decisions. Foraging animals often have access to both self-acquired and socially acquired information about prey. The fringe-lipped bat, Trachops cirrhosus, hunts frogs by approaching the calls that frogs produce to attract mates.We examined howthe reliability of self-acquired prey cues affects social learning of novel prey cues. We trained bats to associate an artificial acoustic cue (mobile phone ringtone) with food rewards. Bats were assigned to treatments in which the trained cue was either an unreliable indicator of reward (rewarded 50% of the presentations) or a reliable indicator (rewarded 100% of the presentations), and they were exposed to a conspecific tutor foraging on a reliable (rewarded 100%) novel cue or to the novel cue with no tutor. Bats whose trained cue was unreliable and who had a tutor were significantly more likely to preferentially approach the novel cue when compared with bats whose trained cue was reliable, and to bats that had no tutor. Reliability of self-acquired prey cues therefore affects social learning of novel prey cues by frog-eating bats. Examining when animals use social information to learn about novel prey is key to understanding the social transmission of foraging innovations. © 2013 The Author(s) Published by the Royal Society.
The twin spot generator for differential Drosophila lineage analysis
Date: 2009-07-28
Creator: Ruth Griffin
Anne Sustar
Marianne Bonvin
Richard Binari
Alberto, del Valle Rodriguez
Amber M. Hohl
Jack R. Bateman
Christians Villalta
Elleard Heffern
Didier Grunwald
Chris Bakal
Claude Desplan
Gerold Schubiger
C. Ting Wu
Norbert Perrimon
Access: Open access
- In Drosophila melanogaster, widely used mitotic recombination-based strategies generate mosaic flies with positive readout for only one daughter cell after division. To differentially label both daughter cells, we developed the twin spot generator (TSG) technique, which through mitotic recombination generates green and red twin spots that are detectable after the first cell division as single cells. We propose wide applications of TSG to lineage and genetic mosaic studies.
Measurements and models of the atmospheric Ar/N2 ratio
Date: 2003-08-01
Creator: Mark Battle
Michael Bender
Melissa B. Hendricks
David T. Ho
Robert, Mika
Galen McKinley
Song Miao Fan
Tegan Blaine
Ralph F. Keeling
Access: Open access
- The Ar/N2 ratio of air measured at 6 globally distributed sites shows annual cycles with amplitudes of 12 to 37 parts in 106. Summertime maxima reflect the atmospheric Ar enrichment driven by seasonal warming and degassing of the oceans. Paired models of air-sea heat fluxes and atmospheric tracer transport predict seasonal cycles in the Ar/N2 ratio that agree with observations, within uncertainties.
Partitioning of the global fossil CO2 sink using a 19-year trend in atmospheric O2
Date: 1999-07-01
Creator: R. L. Langenfelds
R. J. Francey
L. P. Steele
M. Battle
R. F., Keeling
W. F. Budd
Access: Open access
- O2/N2 is measured in the Cape Grim Air Archive (CGAA), a suite of tanks filled with background air at Cape Grim, Tasmania (40.7°S, 144.8°E) between April 1978 and January 1997. Derived trends are compared with published O2/N2 records and assessed against limits on interannual variability of net terrestrial exchanges imposed by trends of δ13C in CO2. Two old samples from 1978 and 1987 and eight from 1996/97 survive critical selection criteria and give a mean 19-year trend in δ(O2/N2) of -16.7 ± 0.5 per meg yr-1, implying net storage of +2.3 ± 0.7 GtC (1015 g carbon) yr-1 of fossil fuel CO2 in the oceans and +0.2 ± 0.9 GtC yr-1 in the terrestrial biosphere. The uptake terms are consistent for both O2/N2 and δ13C tracers if the mean 13C isotopic disequilibrium flux, combining terrestrial and oceanic contributions, is 93 ± 15 GtC ‰ yr-1. Copyright 1999 by the American Geophysical Union.
The tyrosine kinase Abl and its substrate enabled collaborate with the receptor phosphatase Dlar to control motor axon guidance
Date: 1999-01-01
Creator: Zachary Wills
Jack Bateman
Christopher A. Korey
Allen Comer
David, Van Vactor
Access: Open access
- Genetic analysis of growth cone guidance choice points in Drosophila identified neuronal receptor protein tyrosine phosphatases (RPTPs) as key determinants of axon pathfinding behavior. We now demonstrate that the Drosophila Abl tyrosine kinase functions in the intersegmental nerve b (ISNb) motor choice point pathway as an antagonist of the RPTP Dlar. The function of Abl in this pathway is dependent on an intact catalytic domain. We also show that the Abl phosphoprotein substrate Enabled (Ena) is required for choice point navigation. Both Abl and Ena proteins associate with the Dlar cytoplasmic domain and serve as substrates for Dlar in vitro, suggesting that they play a direct role in the Dlar pathway. These data suggest that Dlar, Abl, and Ena define a phosphorylation state-dependent switch that controls growth cone behavior by transmitting signals at the cell surface to the actin cytoskeleton.
Measurement of the B̄→D*lν̄ branching fractions and -Vcb-
Date: 1995-01-01
Creator: B. Barish
M. Chadha
S. Chan
D. F. Cowen
G., Eigen
J. S. Miller
C. O'Grady
J. Urheim
A. J. Weinstein
D. Acosta
M. Athanas
G. Masek
H. P. Paar
J. Gronberg
R. Kutschke
S. Menary
R. J. Morrison
S. Nakanishi
H. N. Nelson
T. K. Nelson
C. Qiao
J. D. Richman
A. Ryd
H. Tajima
D. Sperka
M. S. Witherell
M. Procario
R. Balest
K. Cho
M. Daoudi
W. T. Ford
Access: Open access
- We study the exclusive semileptonic B meson decays B-→D*0l-ν̄ and B̄0→D*+l-ν̄ using data collected with the CLEO II detector at the Cornell Electron-positron Storage Ring (CESR). We present measurements of the branching fractions scrB(B̄0→D*+l-ν̄)= (0.5/f00)[4.49±0.32(stat.)±0.39 (syst.)]% and scrB(B-→D*0l-(ν̄)= (0.5/f+-)[5.13±0.54 (stat) ±0.64 (syst)]%, where f00 and f+- are the neutral and charged B meson production fractions at the Υ(4S) resonance, respectively. Assuming isospin invariance and taking the ratio of charged to neutral B meson lifetimes measured at higher energy machines, we determine the ratio f+-/f00=1.04±0.13 (stat) ±0.12 (syst) ±0.10 (lifetime); further assuming f+-+f00=1 we also determine the partial width Γ(B̄→D*lν̄)=[29.9±1.9 (stat) ±2.7 (syst.) ±2.0 (lifetime)] ns-1 (independent of f+-/f00). From this partial width we calculate B̄→D*lν̄ branching fractions that do not depend on f+-/f00 or the individual B lifetimes, but only on the charged to neutral B lifetime ratio. The product of the CKM matrix element -Vcb- times the normalization of the decay form factor at the point of no recoil of the D* meson, scrF(y=1), is determined from a linear fit to the combined differential decay rate of the exclusive B̄→D*lν̄ decays: -Vcb-scrF(1)=0.0351±0.0019 (stat) ±0.0018 (syst) ±0.0008 (lifetime). The value for -Vcb- is extracted using theoretical calculations of the form factor normalization. © 1995 The American Physical Society.