@article{newell_patisaul_2023, title={Developmental organophosphate flame retardant exposure disrupts adult hippocampal neurogenesis in Wistar rats}, volume={99}, ISSN={["1872-9711"]}, DOI={10.1016/j.neuro.2023.09.009}, abstractNote={Organophosphate flame retardant (OPFR) contamination is ubiquitous and bio-monitoring studies have shown that human exposure is widespread and may be unavoidable. OPFRs bear structural similarities to known neurotoxicants such as organophosphate insecticides and have been shown to have both endocrine disrupting and developmental neurotoxic effects. The perinatal period in rodents represents a critical period in the organization of the developing nervous system and insults during this time can impart profound changes on the trajectory of neural development and function, lasting into adulthood. Adult hippocampal neurogenesis (AHN) facilitates dentate gyrus function and broader hippocampal circuit activity in adults; however, the neurogenic potential of this process in adulthood is vulnerable to disruption by exogenous factors during early life. We sought to assess the impact of OPFRs on AHN in offspring of dams exposed during gestation and lactation. Results indicate that developmental OPFR exposure has significant, sex specific impacts on multiple markers of AHN in the dentate gyrus of rats. In males, OPFR exposure significantly reduced the number of neural progenitors the number of new/immature neurons and reduced dentate gyrus volume. In females, exposure increased the number of neural progenitors, decreased the number of new/immature neurons, but had no significant effect on dentate gyrus volume. These results further elucidate the developmental neurotoxic properties of OPFRs, emphasize the long-term impact of early life OPFR exposure on neural processes, and highlight the importance of including sex as a biological variable in neurotoxicology research.}, journal={NEUROTOXICOLOGY}, author={Newell, Andrew J. and Patisaul, Heather B.}, year={2023}, month={Dec}, pages={104–114} }
 @article{newell_jima_reading_patisaul_2023, title={Machine learning reveals common transcriptomic signatures across rat brain and placenta following developmental organophosphate ester exposure}, volume={7}, ISSN={["1096-0929"]}, DOI={10.1093/toxsci/kfad062}, abstractNote={Abstract
               Toxicogenomics is a critical area of inquiry for hazard identification and to identify both mechanisms of action and potential markers of exposure to toxic compounds. However, data generated by these experiments are highly dimensional and present challenges to standard statistical approaches, requiring strict correction for multiple comparisons. This stringency often fails to detect meaningful changes to low expression genes and/or eliminate genes with small but consistent changes particularly in tissues where slight changes in expression can have important functional differences, such as brain. Machine learning offers an alternative analytical approach for “omics” data that effectively sidesteps the challenges of analyzing highly dimensional data. Using 3 rat RNA transcriptome sets, we utilized an ensemble machine learning approach to predict developmental exposure to a mixture of organophosphate esters (OPEs) in brain (newborn cortex and day 10 hippocampus) and late gestation placenta of male and female rats, and identified genes that informed predictor performance. OPE exposure had sex specific effects on hippocampal transcriptome, and significantly impacted genes associated with mitochondrial transcriptional regulation and cation transport in females, including voltage-gated potassium and calcium channels and subunits. To establish if this holds for other tissues, RNAseq data from cortex and placenta, both previously published and analyzed via a more traditional pipeline, were reanalyzed with the ensemble machine learning methodology. Significant enrichment for pathways of oxidative phosphorylation and electron transport chain was found, suggesting a transcriptomic signature of OPE exposure impacting mitochondrial metabolism across tissue types and developmental epoch. Here we show how machine learning can complement more traditional analytical approaches to identify vulnerable “signature” pathways disrupted by chemical exposures and biomarkers of exposure.}, journal={TOXICOLOGICAL SCIENCES}, author={Newell, Andrew J. and Jima, Dereje and Reading, Benjamin and Patisaul, Heather B.}, year={2023}, month={Jul} }
 @article{newell_kapps_cai_rai_st armour_horman_rock_witchey_greenbaum_patisaul_2023, title={Maternal organophosphate flame retardant exposure alters the developing mesencephalic dopamine system in fetal rat}, volume={191}, ISSN={["1096-0929"]}, DOI={10.1093/toxsci/kfac137}, abstractNote={AbstractOrganophosphate flame retardants (OPFRs) have become the predominant substitution for legacy brominated flame retardants but there is concern about their potential developmental neurotoxicity (DNT). OPFRs readily dissociate from the fireproofed substrate to the environment, and they (or their metabolites) have been detected in diverse matrices including air, water, soil, and biota, including human urine and breastmilk. Given this ubiquitous contamination, it becomes increasingly important to understand the potential effects of OPFRs on the developing nervous system. We have previously shown that maternal exposure to OPFRs results in neuroendocrine disruption, alterations to developmental metabolism of serotonin (5-HT) and axonal extension in male fetal rats, and potentiates adult anxiety-like behaviors. The development of the serotonin and dopamine systems occur in parallel and interact, therefore, we first sought to enhance our prior 5-HT work by first examining the ascending 5-HT system on embryonic day 14 using whole mount clearing of fetal heads and 3-dimensional (3D) brain imaging. We also investigated the effects of maternal OPFR exposure on the development of the mesocortical dopamine system in the same animals through 2-dimensional and 3D analysis following immunohistochemistry for tyrosine hydroxylase (TH). Maternal OPFR exposure induced morphological changes to the putative ventral tegmental area and substantia nigra in both sexes and reduced the overall volume of this structure in males, whereas 5-HT nuclei were unchanged. Additionally, dopaminergic axogenesis was disrupted in OPFR exposed animals, as the dorsoventral spread of ventral telencephalic TH afferents were greater at embryonic day 14, while sparing 5-HT fibers. These results indicate maternal exposure to OPFRs alters the development trajectory of the embryonic dopaminergic system and adds to growing evidence of OPFR DNT.}, number={2}, journal={TOXICOLOGICAL SCIENCES}, author={Newell, Andrew J. and Kapps, Victoria A. and Cai, Yuheng and Rai, Mani Ratnam and St Armour, Genevieve and Horman, Brian M. and Rock, Kylie D. and Witchey, Shannah K. and Greenbaum, Alon and Patisaul, Heather B.}, year={2023}, month={Feb}, pages={357–373} }
 @article{lindquist_feinberg_harrison_loudon_newell_2019, title={The effects of dislocations on crystallographic twins and domain wall motion in magnetite at the Verwey transition}, volume={71}, ISSN={["1880-5981"]}, DOI={10.1186/s40623-018-0981-7}, abstractNote={Pure magnetite experiences a first-order phase transition (the Verwey transition) near 120–125 K wherein the mineral's symmetry changes from cubic to monoclinic. This transformation results in the formation of fine-scale crystallographic twins and is accompanied by a profound change in magnetic properties. The Verwey transition is critical to a variety of applications in environmental magnetism and paleomagnetism because its expression is diagnostic for the presence of stoichiometric (or nearly stoichiometric) magnetite and cycling through the Verwey transition tends to remove the majority of multidomain magnetic remanence. Internal and external stresses demonstrably affect the onset of the Verwey transition. Dislocations create localized internal stress fields and have been cited as a possible source of an altered Verwey transition in deformed samples. To further investigate this behavior, a laboratory-deformed magnetite sample was examined inside a transmission electron microscope as it was cooled through the Verwey transition. Operating the microscope in the Fresnel mode of Lorentz microscopy enabled imaging of the interactions between dislocations, magnetic domain walls, and low-temperature crystallographic twin formation during the phase transition. To relate the observed changes to more readily measurable bulk sample magnetic behavior, low-temperature magnetic measurements were also taken using SQUID magnetometry. This study allows us, for the first time, to observe the Verwey transition in a defect-rich area. Dislocations, and their associated stress fields, impede the development of monoclinic magnetite twin structures during the phase transition and increase the remanence of a magnetite sample after cooling and warming through the Verwey transition.}, journal={EARTH PLANETS AND SPACE}, author={Lindquist, Anna K. and Feinberg, Joshua M. and Harrison, Richard J. and Loudon, James C. and Newell, Andrew J.}, year={2019}, month={Jan} }
 @article{newell_2017, title={Frequency dependence of susceptibility in magnets with uniaxial and triaxial anisotropy}, volume={122}, ISSN={["2169-9356"]}, DOI={10.1002/2017jb014176}, abstractNote={AbstractCharacterization of minerals in rocks and soils provides a window into environmental processes and improves the interpretation of paleomagnetic measurements. Mineral composition, size, and shape can be constrained using magnetic measurements. For small minerals, a promising measurement is the frequency dependence of magnetic susceptibility. The size and shape dependence of the in‐phase component 
 and out‐of‐phase component 
 are derived for arbitrarily oriented superparamagnetic and single‐domain magnets with uniaxial and triaxial anisotropy. In a fluctuating field, a single magnet has a thermal response parallel to the easy axis and instantaneous rotation of the moment perpendicular to it. The size and temperature variations have the same form as in earlier theories in which all the magnets are aligned with the field and can be easily adapted to the methods of Shcherbakov and Fabian (2005) and Egli (2009) for finding size distributions using multiple temperatures and frequencies. These inversions are inherently nonunique and complicated by non‐SD contributions, but some robust constraints can be put on the volume distribution if the commonly used ratio χfd is 10% or greater. The anisotropy of the out‐of‐phase component (opAMS) has the same sense as thermoremanent magnetization (TRM) and can be used to correct the paleofield direction. Along with the anisotropy of the in‐phase component (ipAMS), it can be used to gain quantitative information on the deformation of the host rock. For the line/plane, or March, deformation model, opAMS and ipAMS are calculated and it is shown how they can be used to accurately represent the strain anisotropy.}, number={10}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH}, author={Newell, A. J.}, year={2017}, month={Oct}, pages={7544–7561} }
 @article{bates_newell_niemerg_2017, title={Decoupling highly structured polynomial systems}, volume={79}, ISSN={["0747-7171"]}, DOI={10.1016/j.jsc.2016.07.016}, abstractNote={An efficient technique for finding numerical approximations of isolated solutions of polynomial systems with a particular structure is presented. This structure is quite specific but arises naturally, for example when computing the critical points of a symmetric polynomial energy function. An illustrative example from magnetism is presented, along with some timing comparisons.}, journal={JOURNAL OF SYMBOLIC COMPUTATION}, author={Bates, Daniel J. and Newell, Andrew J. and Niemerg, Matthew E.}, year={2017}, pages={508–515} }
 @article{lindquist_feinberg_harrison_loudon_newell_2015, title={Domain wall pinning and dislocations: Investigating magnetite deformed under conditions analogous to nature using transmission electron microscopy}, volume={120}, ISSN={["2169-9356"]}, DOI={10.1002/2014jb011335}, abstractNote={AbstractIn this study, we deformed samples cut from a single magnetite octahedron and used transmission electron microscopy (TEM) and magnetic measurements to experimentally verify earlier computational models of magnetic domain wall pinning by dislocations and to better understand the nature of dislocations in magnetite. Dislocations in magnetite have been of interest for many decades because they are often cited as a likely source of stable thermoremanent magnetizations in larger multidomain (MD) magnetite grains, so a better understanding of dislocation effects on coercivity in MD magnetite is crucial. TEM imaging shows, for the first time, domain walls sweeping through the magnetite sample and being pinned at dislocations. In agreement with theory, these findings demonstrate that domain walls are more strongly pinned at networks of dislocations than at single dislocations and that domain walls pinned at longer dislocations have higher microcoercivities than those pinned at shorter dislocations. This experimentally illustrates the ability of dislocations to increase the coercivity of larger multidomain magnetite grains. The observed values for microcoercivity and bulk coercivity are in reasonable agreement with theoretical calculations. Burgers vectors were determined for some dislocations to verify that they were in keeping with expected dislocation orientations. The dislocations were found to be primarily located on close‐packed {111} planes within the magnetite. Deformation caused only a minor change in bulk coercivity, but first‐order reversal curve diagrams show populations with increased coercivity not visible in hysteresis loops.}, number={3}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH}, author={Lindquist, A. K. and Feinberg, J. M. and Harrison, R. J. and Loudon, J. C. and Newell, A. J.}, year={2015}, month={Mar}, pages={1415–1430} }
 @article{newell_2009, title={Transition to superparamagnetism in chains of magnetosome crystals}, volume={10}, ISSN={["1525-2027"]}, DOI={10.1029/2009gc002538}, abstractNote={Magnetotactic bacteria use chains of magnetic crystals to orient them in the Earth's field. Magnetic measurements show that these chains are in a single‐domain state with all the moments pointing along the chain axis. Yet many of the crystals in the chains fall in either the multidomain (MD) or the superparamagnetic (SP) size range for isolated crystals. Magnetostatic coupling between crystals keeps the magnetization uniform and prevents thermally assisted transitions between states. The SP critical size for a chain of magnetite crystals is calculated using a new algorithm. The network of stable states and transition states connecting them is determined using a homotopy continuation method. This determines the energy barriers between stable states, and the critical size can then be calculated using a master equation. As the number of crystals in the chain increases, the SP critical volume approaches a limit that is nearly independent of the shape of the crystals. The cube root of this volume is about 10 nm. Most magnetosome crystal sizes are well above this limit. About half of the magnetosome crystals found in sediments would be MD in isolation. However, there is also a population of cubo‐octahedral crystals, a large fraction of which would be SP in isolation. Such crystals are also formed in fresh water by bacteria in the genusMagnetospirillum. The difference in size and shape between the populations of isometric and nonisometric crystals may be related to redox conditions and the choice of magnetoaerotaxis mechanism.}, journal={GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS}, author={Newell, A. J.}, year={2009}, month={Nov} }
 @article{newell_2006, title={Superparamagnetic relaxation times for mixed anisotropy and high energy barriers with intermediate to high damping: 1. Uniaxial axis in a < 001 > direction}, volume={7}, ISSN={["1525-2027"]}, DOI={10.1029/2005gc001146}, abstractNote={The Néel‐Brown theory for superparamagnetic relaxation rates is generalized to ferromagnetic particles with mixed cubic and uniaxial anisotropy. In this article the uniaxial axis is in a 〈001〉 crystallographic direction, while in part 2 it is in a 〈111〉 direction. The calculations are for high energy barriers, so transitions between states (stable equilibria) are rare. Transition rates from an energy minimum across a saddle point are determined by the height of the energy barrier and the shape of the energy surface around these two points. To account for multiple connections between minima, a master equation is solved for the probability distribution and the effect on the magnetic moment is calculated. Some relaxation modes have no effect on the moment. There are as many as five distinct relaxation rates for the probability distribution, but at most two for the moment. One rate is for the component parallel to the uniaxial axis, while the other is for the perpendicular component. These rates are functions of the cubic anisotropy parameterK′1and the uniaxial parameterKu. The double relaxation rate can give rise to phenomena such as partial superparamagnetism and multiple blocking temperatures.}, journal={GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS}, author={Newell, AJ}, year={2006}, month={Mar} }
 @article{newell_2006, title={Superparamagnetic relaxation times for mixed anisotropy and high energy barriers with intermediate to high damping: 2. Uniaxial axis in a < 111 > direction}, volume={7}, ISSN={["1525-2027"]}, DOI={10.1029/2005gc001147}, abstractNote={Superparamagnetic relaxation rates are calculated for ferromagnetic particles with mixed cubic and uniaxial anisotropy. In part 1 the uniaxial axis is in a 〈001〉 crystallographic direction, while in this article it is in a 〈111〉 crystallographic direction. When Ku = 0, there are six remanent states but only one relaxation rate. As Ku increases, the remanent states converge on the uniaxial axis, merging with it at Ku = 0.76 K′1 for K′1 > 0 and at Ku = 0.22 ∣K′1∣ for K′1 < 0. In between the components parallel and perpendicular to the uniaxial axis relax at different rates. The rate for the perpendicular component increases with Ku. If all the remanent states have the same energy, there is a single, decreasing rate for the parallel component. However, for some values of Ku and K′1 there are two states with two different energies. There are then two rates, one decreasing and one increasing. For large Ku the remanence is uniaxial. In this article and part 1 the relaxation rates have an exponential and a prefactor. The prefactors are calculated in the high energy barrier, intermediate‐ to high‐damping approximation. For elongated particles the prefactor is smaller than predicted by the Néel‐Brown theory for uniaxial particles. The predicted relaxation rates are the same order of magnitude as experimental estimates for maghemite and magnetite. Better agreement cannot be expected because order‐of‐magnitude uncertainties still exist in both the experimental and theoretical estimates.}, journal={GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS}, author={Newell, AJ}, year={2006}, month={Mar} }
 @article{newell_2005, title={A high-precision model of first-order reversal curve (FORC) functions for single-domain ferromagnets with uniaxial anisotropy}, volume={6}, ISSN={["1525-2027"]}, DOI={10.1029/2004gc000877}, abstractNote={Plots of the first‐order reversal curve (FORC) function are used to characterize ferromagnetic particles in rocks. The function is based on classical Preisach theory, which represents magnetic hysteresis by elementary loops with displacementHuand half widthHc. Using analytical and numerical integration of single‐particle magnetization curves, a high‐precision FORC function is calculated for a sample with randomly oriented, noninteracting, elongated single‐domain (SD) particles. Some properties of the FORC function are independent of the distribution of particle orientations and shapes. There is a negative peak near theHuaxis, and the FORC function is identically zero forHu> 0. The negative peak, previously attributed to particle interactions, is due to the increasing slope of a reversible magnetization curve near a jump. This peak is seen in experimental FORC functions of SD samples but not of samples with larger particles, probably because of Barkhausen jumps. The second feature is not seen in any experimental FORC function. A spread of the function toHu> 0 can be caused by particle interactions or nonuniform magnetization.}, journal={GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS}, author={Newell, AJ}, year={2005}, month={May} }
 @article{bruneau_newell_crossley_2000, title={Comparative performance of bentgrass species and cultivars in close mown turf}, volume={76}, ISBN={1367-8361}, journal={Journal of Turfgrass Science}, author={Bruneau, A. H. and Newell, A. J. and Crossley, F. M. E.}, year={2000}, pages={63–69} }