@article{tomar_smith_lansky_2022, title={A simple neuronal model with intrinsic saturation of the firing frequency}, volume={222}, ISSN={["1872-8324"]}, DOI={10.1016/j.biosystems.2022.104780}, abstractNote={We present a comparison of the intrinsic saturation of firing frequency in four simple neural models: leaky integrate-and-fire model, leaky integrate-and-fire model with reversal potentials, two-point leaky integrate-and-fire model, and a two-point leaky integrate-and-fire model with reversal potentials. "Two-point" means that the equivalent circuit has two nodes (dendritic and somatic) instead of one (somatic only). The results suggest that the reversal potential increases the slope of the "firing rate vs input" curve due to a smaller effective membrane time constant, but does not necessarily induce saturation of the firing rate. The two-point model without the reversal potential does not limit the voltage or the firing rate. In contrast to the previous models, the two-point model with the reversal potential limits the asymptotic voltage and the firing rate, which is the main result of this paper. The case of excitatory inputs is considered first and followed by the case of both excitatory and inhibitory inputs.}, journal={BIOSYSTEMS}, author={Tomar, Rimjhim and Smith, Charles E. and Lansky, Petr}, year={2022}, month={Dec} }
 @article{butler_ehling_barbar_thomas_hughes_smith_pogorelov_aryal_wetsel_lascelles_et al._2017, title={Distinct neuronal populations in the basolateral and central amygdala are activated with acute pain, conditioned fear, and fear-conditioned analgesia}, volume={661}, ISSN={["1872-7972"]}, url={https://dx.doi.org/10.1016/j.neulet.2017.09.025}, DOI={10.1016/j.neulet.2017.09.025}, abstractNote={Fear-conditioned analgesia (FCA) is modulated by brain areas involved in the descending inhibitory pain pathway such as the basolateral (BLA) and central amygdala (CEA). The BLA contains Ca2+/calmodulin-dependent protein kinase II (CaMKII) and parvalbumin (PV) neurons. CEA neurons are primarily inhibitory (GABAergic) that comprise enkephalin (ENK) interneurons and corticotropin-releasing factor (CRF) - neurons that project to the periaqueductal grey. The purpose of our experiment was to determine the pattern of activation of CaMKII/PV and ENK/CRF neurons following the expression of acute pain, conditioned fear, and FCA. A significant reduction was observed in nociceptive behaviors in mice re-exposed to a contextually-aversive environment. Using NeuN and cFos as markers for activated neurons, CaMKII, PV, ENK, or CRF were used to identify neuronal subtypes. We find that mice expressing conditioned fear displayed an increase in c-Fos/CaMKII co-localization in the lateral amygdala and BLA compared to controls. Additionally a significant increase in cFos/CRF co-localization was observed in mice expressing FCA. These results show that amygdala processing of conditioned contextual aversive, nociceptive, and FCA behaviors involve different neuronal phenotypes and neural circuits between, within, and from various amygdala nuclei. This information will be important in developing novel therapies for treating pain and emotive disorders in humans.}, journal={NEUROSCIENCE LETTERS}, author={Butler, R. K. and Ehling, S. and Barbar, M. and Thomas, J. and Hughes, M. A. and Smith, C. E. and Pogorelov, V. M. and Aryal, D. K. and Wetsel, W. C. and Lascelles, B. D. X. and et al.}, year={2017}, month={Nov}, pages={11–17} }
 @article{enomoto_kigin_bledsoe_slone_hash_smith_lascelles_2017, title={Pilot evaluation of a novel unilateral onychectomy model and efficacy of an extended release buprenorphine product}, volume={13}, journal={BMC Veterinary Research}, author={Enomoto, M. and Kigin, P. D. and Bledsoe, D. and Slone, R. and Hash, J. and Smith, C. E. and Lascelles, B. D. X.}, year={2017} }
 @article{smith_kolar_boyette_chinn_smith_gangadharan_zhang_2012, title={Advanced oxidation of toluene using Ni-olivine catalysts: Part 1. syntheses, characterization, and evaluation of Ni-olivine catalysts for toluene oxidation}, volume={55}, number={3}, journal={Transactions of the ASABE}, author={Smith, V. M. and Kolar, P. and Boyette, M. D. and Chinn, M. and Smith, C. and Gangadharan, R. and Zhang, G.}, year={2012}, pages={1013–1024} }
 @article{hosein_breidt_smith_2011, title={Modeling the Effects of Sodium Chloride, Acetic Acid, and Intracellular pH on Survival of Escherichia coli O157:H7}, volume={77}, ISSN={["1098-5336"]}, DOI={10.1128/aem.02136-10}, abstractNote={ABSTRACT}, number={3}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Hosein, Althea M. and Breidt, Frederick, Jr. and Smith, Charles E.}, year={2011}, month={Feb}, pages={889–895} }
 @article{tzeng_zhang_pongpanich_smith_mccarthy_sale_worrall_hsu_thomas_sullivan_2011, title={Studying Gene and Gene-Environment Effects of Uncommon and Common Variants on Continuous Traits: A Marker-Set Approach Using Gene-Trait Similarity Regression}, volume={89}, ISSN={["1537-6605"]}, DOI={10.1016/j.ajhg.2011.07.007}, abstractNote={Genomic association analyses of complex traits demand statistical tools that are capable of detecting small effects of common and rare variants and modeling complex interaction effects and yet are computationally feasible. In this work, we introduce a similarity-based regression method for assessing the main genetic and interaction effects of a group of markers on quantitative traits. The method uses genetic similarity to aggregate information from multiple polymorphic sites and integrates adaptive weights that depend on allele frequencies to accomodate common and uncommon variants. Collapsing information at the similarity level instead of the genotype level avoids canceling signals that have the opposite etiological effects and is applicable to any class of genetic variants without the need for dichotomizing the allele types. To assess gene-trait associations, we regress trait similarities for pairs of unrelated individuals on their genetic similarities and assess association by using a score test whose limiting distribution is derived in this work. The proposed regression framework allows for covariates, has the capacity to model both main and interaction effects, can be applied to a mixture of different polymorphism types, and is computationally efficient. These features make it an ideal tool for evaluating associations between phenotype and marker sets defined by linkage disequilibrium (LD) blocks, genes, or pathways in whole-genome analysis.}, number={2}, journal={AMERICAN JOURNAL OF HUMAN GENETICS}, author={Tzeng, Jung-Ying and Zhang, Daowen and Pongpanich, Monnat and Smith, Chris and McCarthy, Mark I. and Sale, Michele M. and Worrall, Bradford B. and Hsu, Fang-Chi and Thomas, Duncan C. and Sullivan, Patrick F.}, year={2011}, month={Aug}, pages={277–288} }
 @article{alpizar-jara_smith_2008, title={A continuous time version and a generalization of a Markov-recapture model for trapping experiments}, volume={214}, ISSN={["1879-3134"]}, DOI={10.1016/j.mbs.2008.01.004}, abstractNote={Markov-recapture population estimates: a tool for improving interpretation of trapping experiments}, number={1-2}, journal={MATHEMATICAL BIOSCIENCES}, author={Alpizar-Jara, Russell and Smith, Charles E.}, year={2008}, pages={11–19} }
 @article{wang_smith_atchley_2007, title={Application of complex demodulation on bZIP and bHLH-PAS protein domains}, volume={207}, DOI={10.1016/j.mbs.2007.01.004}, abstractNote={Proteins are built with molecular modular building blocks such as an alpha-helix, beta-sheet, loop region and other structures. This is an economical way of constructing complex molecules. Periodicity analysis of protein sequences has allowed us to obtain meaningful information concerning their structure, function and evolution. In this work, complex demodulation (CDM) is introduced to detect functional regions in protein sequences data. More specifically, we analyzed bZIP and bHLH-PAS protein domains. Complex demodulation provided insightful information about changing amplitudes of periodic components in protein sequences. Furthermore, it was found that the local amplitude minimum or local amplitude maximum of the 3.6-aa periodic component is associated with protein structural or functional information due to the observation that the extrema are mainly located in the boundary area of two structural or functional regions.}, number={2}, journal={Mathematical Biosciences}, author={Wang, Z. and Smith, C. E. and Atchley, W. R.}, year={2007}, pages={204–218} }
 @article{sacerdote_smith_2004, title={Almost sure comparisons for first passage times of diffusion processes through boundaries}, volume={6}, ISSN={["1573-7713"]}, DOI={10.1023/B:MCAP.0000026563.27820.ff}, number={3}, journal={METHODOLOGY AND COMPUTING IN APPLIED PROBABILITY}, author={Sacerdote, L and Smith, CE}, year={2004}, month={Sep}, pages={323–341} }
 @unpublished{smith_2002, title={Ama no gawa}, volume={56}, number={2002 July}, journal={Haiku Alpha}, author={Smith, C.}, year={2002}, pages={202} }
 @inbook{smith_2002, title={Kezu de tadoru sakabiki haijin maikan}, booktitle={Kezu de tadoru sakabiki haijin maikan Mainichi shimbun = Poems from the 6th annual Mainichi Haiku Contest}, publisher={Tokyo: Mainichi shimbun}, author={Smith, C. E.}, year={2002}, pages={202} }
 @article{riviere_smith_budsaba_brooks_olajos_salem_monteiro-riviere_2001, title={Use of methyl salicylate as a simulant to predict the percutaneous absorption of sulfur mustard}, volume={21}, ISSN={["1099-1263"]}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000167916500002&KeyUID=WOS:000167916500002}, DOI={10.1002/jat.718}, abstractNote={Abstract}, number={2}, journal={JOURNAL OF APPLIED TOXICOLOGY}, author={Riviere, JE and Smith, CE and Budsaba, K and Brooks, JD and Olajos, EJ and Salem, H and Monteiro-Riviere, NA}, year={2001}, pages={91–99} }
 @article{sacerdote_smith_2000, title={A qualitative comparison of some diffusion models for neural activity via stochastic ordering}, volume={83}, ISSN={["0340-1200"]}, DOI={10.1007/s004220000179}, abstractNote={A number of diffusion processes have been proposed as a continuous analog of Stein's model for the subthreshold membrane potential of a neuron. Interspike intervals are then described as the first-passage-time of the corresponding diffusion model through a suitable threshold. Various biological considerations suggest the use of more sophisticated models in lieu of the Ornstein-Uhlenbeck model. However, the advantages of the additional complexity are not always clear. Comparisons among different models generally use numerical methods in specific examples without a general sensitivity analysis on the role of the model parameters. Here, we compare the distribution of interspike intervals from different models using the method of stochastic ordering. The qualitative comparison of the role of each parameter extends the results obtained from numerical simulations. One result on neurons with high positive net excitation is that the reversal potential models considered do not greatly differ from the Ornstein-Uhlenbeck model. For neurons with increased inhibition, the models give greater differences among the interspike interval distributions. In particular, when the mean trajectories are matched, the Feller model gives shorter times than the Ornstein-Uhlenbeck model but longer times than our double reversal potential model.}, number={6}, journal={BIOLOGICAL CYBERNETICS}, author={Sacerdote, L and Smith, CE}, year={2000}, month={Dec}, pages={543–551} }
 @article{budsaba_smith_riviere_2000, title={Compass plots: A combination of star plot and analysis of means to visualize significant interactions in complex toxicology studies}, volume={10}, ISSN={["1051-7235"]}, DOI={10.1080/105172300750048764}, abstractNote={The Compass Plot, a new graphical methodthat combines the advantages of the star plot andthe analysis of means (ANOM), has beenintroducedfordisplaying the results of experiments. Incontrast to the star plot, this plot allows statistical inferences to be made for treatment and for factor effects. In contrast to ANOM, this plot is good for comparison in multiresponse experiments, a scenario becoming more commonplace in toxicology with the advent of increasing numbers of chemical mixture studies. An example of a 2 3 factorial chemical exposure experiment is considered here.}, number={4}, journal={TOXICOLOGY METHODS}, author={Budsaba, K and Smith, CE and Riviere, JE}, year={2000}, pages={313–332} }
 @article{gutkin_smith_2000, title={Conditions for noise reduction and stable encoding of spatial structure by cortical neural networks}, volume={82}, ISSN={["0340-1200"]}, DOI={10.1007/s004220050599}, abstractNote={Cortical circuits have been proposed to encode information by forming stable spatially structured attractors. Experimentally in the primary somatosensory cortex of the monkey, temporally invariant stimuli lead to spatially structured activity patterns. The purpose of this work is to study a recurrent cortical neural network model with lateral inhibition and examine what effect additive random noise has on the networks' ability to form stable spatially structured representations of the stimulus pattern. We show numerically that this network performs edge enhancement and forms statistically stationary, spatially structured responses when the lateral inhibition is of moderate strength. We then derive analytical conditions on the connectivity matrix that ensure stochasticly stable encoding of the stimulus spatial structure by the network. For stimuli whose strength falls in the near linear region of the sigmoid, we are able to give explicit conditions on the eigenvalues of the connection matrix. Finally, we prove that a network with a connection matrix, where the total excitation and inhibition impinging upon a neural unit are nearly balanced, will yield stable spatial attractor responses.}, number={6}, journal={BIOLOGICAL CYBERNETICS}, author={Gutkin, BS and Smith, CE}, year={2000}, month={Jun}, pages={469–475} }
 @article{sacerdote_smith_2000, title={New parameter relationships determined via stochastic ordering for spike activity in a reversal potential neural model}, volume={58}, ISSN={["0303-2647"]}, DOI={10.1016/s0303-2647(00)00107-6}, abstractNote={Purpose of this work is to study the dependence of interspike interval distribution on the model parameters when use is made of the Feller diffusion process to describe the subthreshold membrane potential of a neuron. To this aim we make use of a new approach, namely the ordering of first passage times. The functional dependence among the model parameters (e.g, membrane time constant, reversal potential, etc.) resulting from the ordering criteria employed and from the study of mean trajectory plots is analyzed into detail for four different scenario.}, number={1-3}, journal={BIOSYSTEMS}, author={Sacerdote, L and Smith, CE}, year={2000}, pages={59–65} }
 @article{smith_lansky_lung_1997, title={Cycle time and residence time density approximations in a stochastic model for circulatory transport}, volume={59}, DOI={10.1007/bf02459468}, abstractNote={The concentration of a drug in the circulatory system is studied under two different elimination strategies. The first strategy—geometric elimination—is the classical one which assumes a constant elimination rate per cycle. The second strategy—Poisson elimination—assumes that the elimination rate changes during the process of elimination. The problem studied here is to find a relationship between the residence-time distribution and the cycle-time distribution for a given rule of elimination. While the presented model gives this relationship in terms of Laplace-Stieltjes transform, the aim here is to determine the shapes of the corresponding probability density functions. From experimental data, we expect positively skewed, gamma-like distributions for the residence time of the drug in the body. Also, as some elimination parameter in the model approaches a limit, the exponential distribution often arises. Therefore, we use laguerre series expansions, which yield a parsimonious approximation of positively skewed probability densities that are close to a gamma distribution. The coefficients in the expansion are determined by the central moments, which can be obtained from experimental data or as a consequence of theoretical assumptions. The examples presented show that gamma-like densities arise for a diverse set of cycle-time distributions and under both elimination rules.}, number={1}, journal={Bulletin of Mathematical Biology}, author={Smith, C. E. and Lansky, P. and Lung, T.-H.}, year={1997}, pages={1–22} }