Publications by authors named "Philip Long"

Type A γ-aminobutyric acid receptors (GABARs) represent a family of pentameric GABA-gated Cl/HCO ion channels which mediate inhibitory transmission in the central nervous system. Cell surface expression of GABARs, a prerequisite for their function, is dependent on the appropriate assembly of the receptor subunits and their transient interactions with molecular chaperones within the endoplasmic reticulum (ER) and Golgi apparatus. Here, we describe a highly conserved amino acid sequence within the extracellular N-terminal domain of the receptor subunits adjoining the first transmembrane domain as a region important for GABAR processing within the ER.

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van Rooyen, Menon, and Williamson (2015) introduced a notion of convex loss functions being robust to random classification noise and established that the "unhinged" loss function is robust in this sense. In this letter, we study the accuracy of binary classifiers obtained by minimizing the unhinged loss and observe that even for simple linearly separable data distributions, minimizing the unhinged loss may only yield a binary classifier with accuracy no better than random guessing.

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In remote applications that mandate human supervision, shared control can prove vital by establishing a harmonious balance between the high-level cognition of a user and the low-level autonomy of a robot. Though in practice, achieving this balance is a challenging endeavor that largely depends on whether the operator effectively interprets the underlying shared control. Inspired by recent works on using immersive technologies to expose the internal shared control, we develop a virtual reality system to visually guide human-in-the-loop manipulation.

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Nuclear energy will play a critical role in meeting clean energy targets worldwide. However, nuclear environments are dangerous for humans to operate in due to the presence of highly radioactive materials. Robots can help address this issue by allowing remote access to nuclear and other highly hazardous facilities under human supervision to perform inspection and maintenance tasks during normal operations, help with clean-up missions, and aid in decommissioning.

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The phenomenon of benign overfitting is one of the key mysteries uncovered by deep learning methodology: deep neural networks seem to predict well, even with a perfect fit to noisy training data. Motivated by this phenomenon, we consider when a perfect fit to training data in linear regression is compatible with accurate prediction. We give a characterization of linear regression problems for which the minimum norm interpolating prediction rule has near-optimal prediction accuracy.

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We analyze the joint probability distribution on the lengths of the vectors of hidden variables in different layers of a fully connected deep network, when the weights and biases are chosen randomly according to gaussian distributions. We show that if the activation function satisfies a minimal set of assumptions, satisfied by all activation functions that we know that are used in practice, then, as the width of the network gets large, the "length process" converges in probability to a length map that is determined as a simple function of the variances of the random weights and biases and the activation function . We also show that this convergence may fail for that violate our assumptions.

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The recruitment of inhibitory GABA receptors to neuronal synapses requires a complex interplay between receptors, neuroligins, the scaffolding protein gephyrin and the GDP-GTP exchange factor collybistin (CB). Collybistin is regulated by protein-protein interactions at the N-terminal SH3 domain, which can bind neuroligins 2/4 and the GABAR α2 subunit. Collybistin also harbors a RhoGEF domain which mediates interactions with gephyrin and catalyzes GDP-GTP exchange on Cdc42.

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We analyze algorithms for approximating a function mapping to using deep linear neural networks, that is, that learn a function parameterized by matrices and defined by . We focus on algorithms that learn through gradient descent on the population quadratic loss in the case that the distribution over the inputs is isotropic. We provide polynomial bounds on the number of iterations for gradient descent to approximate the least-squares matrix , in the case where the initial hypothesis has excess loss bounded by a small enough constant.

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Academic cheating has become a pervasive practice from primary schools to university. This study aims at investigating this phenomenon through a nomological network which integrates different theoretical frameworks and models, such as trait and social-cognitive theories and models regarding the approaches to learning and contextual/normative environment. Results on a sample of more than 200 Italian university students show that the Amoral Manipulation facet of Machiavellianism, Academic Moral Disengagement, Deep Approach to Learning, and Normative Academic Cheating are significantly associated with Individual Academic Cheating.

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Biostimulation to induce reduction of soluble U(VI) to relatively immobile U(IV) is an effective strategy for decreasing aqueous U(VI) concentrations in contaminated groundwater systems. If oxidation of U(IV) occurs following the biostimulation phase, U(VI) concentrations increase, challenging the long-term effectiveness of this technique. However, detecting U(IV) oxidation through dissolved U concentrations alone can prove difficult in locations with few groundwater wells to track the addition of U to a mass of groundwater.

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The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) Project (www.toxpath.org/inhand.

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Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations.

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Non-syndromal X-linked intellectual disability (NS-XLID) represents a broad group of clinical disorders in which ID is the only clinically consistent manifestation. Although in many cases either chromosomal linkage data or knowledge of the >100 existing XLID genes has assisted mutation discovery, the underlying cause of disease remains unresolved in many families. We report the resolution of a large family (K8010) with NS-XLID, with variable macrocephaly and macro-orchidism.

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Disease gene discovery in neurodevelopmental disorders, including X-linked intellectual disability (XLID) has recently been accelerated by next-generation DNA sequencing approaches. To date, more than 100 human X chromosome genes involved in neuronal signaling pathways and networks implicated in cognitive function have been identified. Despite these advances, the mutations underlying disease in a large number of XLID families remained unresolved.

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The Rifle alluvial aquifer along the Colorado River in west central Colorado contains fine-grained, diffusion-limited sediment lenses that are substantially enriched in organic carbon and sulfides, as well as uranium, from previous milling operations. These naturally reduced zones (NRZs) coincide spatially with a persistent uranium groundwater plume. There is concern that uranium release from NRZs is contributing to plume persistence or will do so in the future.

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Understanding which organisms are capable of reducing uranium at historically contaminated sites provides crucial information needed to evaluate treatment options and outcomes. One approach is determination of the bacteria which directly respond to uranium addition. In this study, uranium amendments were made to groundwater samples from a site of ongoing biostimulation with acetate.

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Article Synopsis
  • - The KCC2 protein, linked to the SLC12A5 gene, is essential for regulating chloride ions in the brain, which helps control fast synaptic inhibition.
  • - Researchers discovered mutations in the SLC12A5 gene that cause a severe form of epilepsy known as epilepsy of infancy with migrating focal seizures (EIMFS).
  • - Problems with KCC2, such as reduced surface expression and impaired function, lead to disrupted synaptic inhibition and increased neuron activity, contributing to this early-onset epilepsy.
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Oxidative dissolution controls uranium release to (sub)oxic pore waters from biogenic uraninite produced by natural or engineered processes, such as bioremediation. Laboratory studies show that uraninite dissolution is profoundly influenced by dissolved oxygen (DO), carbonate, and solutes such as Ca(2+). In complex and heterogeneous subsurface environments, the concentrations of these solutes vary in time and space.

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The Department of Energy's Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect.

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Article Synopsis
  • The study examines in situ bioreduction of U(VI) in Rifle, Colorado, by deploying sediment-filled columns in a groundwater well and stimulating microbial growth with a mixture of groundwater, soluble U(VI), and acetate.
  • Approximately 90% of the uranium was successfully reduced to U(IV) across different redox conditions, with noncrystalline U(IV) making up about two-thirds of the reduced uranium.
  • The findings underline the need to account for noncrystalline U(IV) formation when developing remediation strategies due to its higher susceptibility to remobilization and reoxidation compared to crystalline forms.
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We aim to understand the scale-dependent evolution of uranium bioreduction during a field experiment at a former uranium mill site near Rifle, Colorado. Acetate was injected to stimulate Fe-reducing bacteria (FeRB) and to immobilize aqueous U(VI) to insoluble U(IV). Bicarbonate was coinjected in half of the domain to mobilize sorbed U(VI).

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Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source.

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Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, CO, USA, and document interlinked microbial roles in geochemical cycling.

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Removal of selenium from groundwater was documented during injection of acetate into a uranium-contaminated aquifer near Rifle, Colorado (USA). Bioreduction of aqueous selenium to its elemental form (Se0) concentrated it within mineralized biofilms affixed to tubing used to circulate acetate-amended groundwater. Scanning and transmission electron microscopy revealed close association between Se0 precipitates and cell surfaces, with Se0 aggregates having a diameter of 50-60 nm.

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The multifunctional protein osteopontin (OPN) is expressed in the substantia nigra (SN) and protects nigral dopaminergic neurones against toxic insult in animal models of Parkinson's disease, although the mechanisms involved are uncertain. In the periphery, OPN regulates inflammatory processes by interacting with integrin and CD44 receptors but the presence and distribution of these sites in SN is unknown. We investigated the expression of integrin receptor subunits and CD44 receptors in the normal SN and after induction of inflammation by lipopolysaccharide (LPS), and their interaction with OPN.

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