Control of cell surface expression of GABAA receptors by a conserved region at the end of the N-terminal extracellular domain of receptor subunits.

Type A γ-aminobutyric acid receptors (GABAARs) represent a family of pentameric GABA-gated Cl-/HCO3- ion channels which mediate inhibitory transmission in the central nervous system. Cell surface expression of GABAARs, 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 GABAAR processing within the ER. Modifications of this region in the α1, ß3, and γ2 subunits using insertion or site-directed mutagenesis impaired GABAAR trafficking to the cell surface in heterologous cell systems although they had no effect on the subunit assembly. We found that mutated receptors accumulated in the ER where they were shown to associate with chaperones calnexin, BiP, and Grp94. However, their surface expression was increased when ER-associated degradation or proteosome function was inhibited, while modulation of ER calcium stores had little effect. When compared to the wt, mutated receptors showed decreased interaction with calnexin, similar binding to BiP, and increased association with Grp94. Structural modeling of calnexin interaction with the wt or mutated GABAAR revealed that disruption in structure caused by mutations in the conserved region adjoining the first transmembrane domain may impair calnexin binding. Thus, this previously uncharacterized region plays an important role in intracellular processing of GABAARs at least in part by stabilizing their interaction with calnexin.

The Perils of Being Unhinged: On the Accuracy of Classifiers Minimizing a Noise-Robust Convex Loss.

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.

Motion Polytopes in Virtual Reality for Shared Control in Remote Manipulation Applications.

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. Our implementation of shared control teleoperation employs end effector manipulability polytopes, which are geometrical constructs that embed joint limit and environmental constraints. These constructs capture a holistic view of the constrained manipulator's motion and can thus be visually represented as feedback for users on their operable space of movement. To assess the efficacy of our proposed approach, we consider a teleoperation task where users manipulate a screwdriver attached to a robotic arm's end effector. A pilot study with prospective operators is first conducted to discern which graphical cues and virtual reality setup are most preferable. Feedback from this study informs the final design of our virtual reality system, which is subsequently evaluated in the actual screwdriver teleoperation experiment. Our experimental findings support the utility of using polytopes for shared control teleoperation, but hint at the need for longer-term studies to garner their full benefits as virtual guides.

A Holistic Approach to Human-Supervised Humanoid Robot Operations in Extreme Environments.

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. This paper presents our research to help realize humanoid robots in supervisory roles in nuclear environments. Our research focuses on National Aeronautics and Space Administration (NASA's) humanoid robot, Valkyrie, in the areas of constrained manipulation and motion planning, increasing stability using support contact, dynamic non-prehensile manipulation, locomotion on deformable terrains, and human-in-the-loop control interfaces.

Benign overfitting in linear regression.

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. The characterization is in terms of two notions of the effective rank of the data covariance. It shows that overparameterization is essential for benign overfitting in this setting: the number of directions in parameter space that are unimportant for prediction must significantly exceed the sample size. By studying examples of data covariance properties that this characterization shows are required for benign overfitting, we find an important role for finite-dimensional data: the accuracy of the minimum norm interpolating prediction rule approaches the best possible accuracy for a much narrower range of properties of the data distribution when the data lie in an infinite-dimensional space vs. when the data lie in a finite-dimensional space with dimension that grows faster than the sample size.

On the Effect of the Activation Function on the Distribution of Hidden Nodes in a Deep Network.

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 φ 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 φ. We also show that this convergence may fail for φ that violate our assumptions. We show how to use this analysis to choose the variance of weight initialization, depending on the activation function, so that hidden variables maintain a consistent scale throughout the network.

Mutation p.R356Q in the Collybistin Phosphoinositide Binding Site Is Associated With Mild Intellectual Disability.

The recruitment of inhibitory GABAA 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 GABAAR α2 subunit. Collybistin also harbors a RhoGEF domain which mediates interactions with gephyrin and catalyzes GDP-GTP exchange on Cdc42. Lastly, collybistin has a pleckstrin homology (PH) domain, which binds phosphoinositides, such as phosphatidylinositol 3-phosphate (PI3P/PtdIns3P) and phosphatidylinositol 4-monophosphate (PI4P/PtdIns4P). PI3P located in early/sorting endosomes has recently been shown to regulate the postsynaptic clustering of gephyrin and GABAA receptors and consequently the strength of inhibitory synapses in cultured hippocampal neurons. This process is disrupted by mutations in the collybistin gene (ARHGEF9), which cause X-linked intellectual disability (XLID) by a variety of mechanisms converging on disrupted gephyrin and GABAA receptor clustering at central synapses. Here we report a novel missense mutation (chrX:62875607C>T, p.R356Q) in ARHGEF9 that affects one of the two paired arginine residues in the PH domain that were predicted to be vital for binding phosphoinositides. Functional assays revealed that recombinant collybistin CB3SH3- R356Q was deficient in PI3P binding and was not able to translocate EGFP-gephyrin to submembrane microaggregates in an in vitro clustering assay. Expression of the PI3P-binding mutants CB3SH3- R356Q and CB3SH3- R356N/R357N in cultured hippocampal neurones revealed that the mutant proteins did not accumulate at inhibitory synapses, but instead resulted in a clear decrease in the overall number of synaptic gephyrin clusters compared to controls. Molecular dynamics simulations suggest that the p.R356Q substitution influences PI3P binding by altering the range of structural conformations adopted by collybistin. Taken together, these results suggest that the p.R356Q mutation in ARHGEF9 is the underlying cause of XLID in the probands, disrupting gephyrin clustering at inhibitory GABAergic synapses via loss of collybistin PH domain phosphoinositide binding.

Gradient Descent with Identity Initialization Efficiently Learns Positive-Definite Linear Transformations by Deep Residual Networks.

We analyze algorithms for approximating a function f(x)=Φx mapping ℜd to ℜd using deep linear neural networks, that is, that learn a function h parameterized by matrices Θ1,…,ΘL and defined by h(x)=ΘLΘL-1…Θ1x . 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 Φ , in the case where the initial hypothesis Θ1=…=ΘL=I has excess loss bounded by a small enough constant. We also show that gradient descent fails to converge for Φ whose distance from the identity is a larger constant, and we show that some forms of regularization toward the identity in each layer do not help. If Φ is symmetric positive definite, we show that an algorithm that initializes Θi=I learns an ε -approximation of f using a number of updates polynomial in L , the condition number of Φ , and log(d/ε) . In contrast, we show that if the least-squares matrix Φ is symmetric and has a negative eigenvalue, then all members of a class of algorithms that perform gradient descent with identity initialization, and optionally regularize toward the identity in each layer, fail to converge. We analyze an algorithm for the case that Φ satisfies u⊤Φu>0 for all u but may not be symmetric. This algorithm uses two regularizers: one that maintains the invariant u⊤ΘLΘL-1…Θ1u>0 for all u and the other that "balances" Θ1,…,ΘL so that they have the same singular values.

Machiavellian Ways to Academic Cheating: A Mediational and Interactional Model.

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. Moreover, results show a significant latent interaction effect between Normative Academic Cheating and Amoral Manipulation Machiavellianism: "amoral Machiavellians" students are more prone to resort to Academic Cheating in contexts where Academic Cheating is adopted as a practice by their peers, while this effect is not significant in contexts where Academic Cheating is not normative. Results also show that Academic Moral Disengagement and Deep Approach to learning partially mediate the relationship between Amoral Manipulation and Academic Cheating. Practical implications of these results are discussed.

Field Application of 238U/235U Measurements To Detect Reoxidation and Mobilization of U(IV).

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. We propose the 238U/235U ratio of aqueous U as an independent, reliable tracer of U(IV) remobilization via oxidation or mobilization of colloids. Reduction of U(VI) produces 238U-enriched U(IV), whereas remobilization of solid U(IV) should not induce isotopic fractionation. The incorporation of remobilized U(IV) with a high 238U/235U ratio into the aqueous U(VI) pool produces an increase in 238U/235U of aqueous U(VI). During several injections of nitrate to induce U(IV) oxidation, 238U/235U consistently increased, suggesting 238U/235U is broadly applicable for detecting mobilization of U(IV).

Nonproliferative and Proliferative Lesions of the Rat and Mouse Skeletal Tissues (Bones, Joints, and Teeth).

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) Project (www.toxpath.org/inhand.asp) is an initiative of the Societies of Toxicological Pathology from Europe (ESTP), Great Britain (BSTP), Japan (JSTP) and North America (STP) to develop an internationally accepted nomenclature for proliferative and nonproliferative lesions in laboratory animals. The purpose of this publication is to provide a standardized nomenclature for classifying microscopic lesions observed in the skeletal tissues and teeth of laboratory rats and mice, with color photomicrographs illustrating examples of many common lesions. The standardized nomenclature presented in this document is also available on the internet (http://www.goreni.org/). Sources of material were databases from government, academic and industrial laboratories throughout the world.

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

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. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O.

Physico-Chemical Heterogeneity of Organic-Rich Sediments in the Rifle Aquifer, CO: Impact on Uranium Biogeochemistry.

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. To better define the physical extent, heterogeneity and biogeochemistry of these NRZs, we investigated sediment cores from five neighboring wells. The main NRZ body exhibited uranium concentrations up to 100 mg/kg U as U(IV) and contains ca. 286 g of U in total. Uranium accumulated only in areas where organic carbon and reduced sulfur (as iron sulfides) were present, emphasizing the importance of sulfate-reducing conditions to uranium retention and the essential role of organic matter. NRZs further exhibited centimeter-scale variations in both redox status and particle size. Mackinawite, greigite, pyrite and sulfate coexist in the sediments, indicating that dynamic redox cycling occurs within NRZs and that their internal portions can be seasonally oxidized. We show that oxidative U(VI) release to the aquifer has the potential to sustain a groundwater contaminant plume for centuries. NRZs, known to exist in other uranium-contaminated aquifers, may be regionally important to uranium persistence.

Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.

The potassium-chloride co-transporter KCC2, encoded by SLC12A5, plays a fundamental role in fast synaptic inhibition by maintaining a hyperpolarizing gradient for chloride ions. KCC2 dysfunction has been implicated in human epilepsy, but to date, no monogenic KCC2-related epilepsy disorders have been described. Here we show recessive loss-of-function SLC12A5 mutations in patients with a severe infantile-onset pharmacoresistant epilepsy syndrome, epilepsy of infancy with migrating focal seizures (EIMFS). Decreased KCC2 surface expression, reduced protein glycosylation and impaired chloride extrusion contribute to loss of KCC2 activity, thereby impairing normal synaptic inhibition and promoting neuronal excitability in this early-onset epileptic encephalopathy.

Identification of Bacteria Synthesizing Ribosomal RNA in Response to Uranium Addition During Biostimulation at the Rifle, CO Integrated Field Research Site.

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. The active microbes in the planktonic phase were deduced by monitoring ribosomes production via RT-PCR. The results indicated several microorganisms were synthesizing ribosomes in proportion with uranium amendment up to 2 µM. Concentrations of U (VI) >2 µM were generally found to inhibit ribosome synthesis. Two active bacteria responding to uranium addition in the field were close relatives of Desulfobacter postgateii and Geobacter bemidjiensis. Since RNA content often increases with growth rate, our findings suggest it is possible to rapidly elucidate active bacteria responding to the addition of uranium in field samples and provides a more targeted approach to stimulate specific populations to enhance radionuclide reduction in contaminated sites.

Long-term in situ oxidation of biogenic uraninite in an alluvial aquifer: impact of dissolved oxygen and calcium.

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. Knowledge of dissolution processes and kinetics occurring over the long-term under such conditions is needed to predict subsurface uranium behavior and optimize the selection and performance of uraninite-based remediation technologies over multiyear periods. We have assessed dissolution of biogenic uraninite deployed in wells at the Rifle, CO, DOE research site over a 22 month period. Uraninite loss rates were highly sensitive to DO, with near-complete loss at >0.6 mg/L over this period but no measurable loss at lower DO. We conclude that uraninite can be stable over decadal time scales in aquifers under low DO conditions. U(VI) solid products were absent over a wide range of DO values, suggesting that dissolution proceeded through complexation and removal of oxidized surface uranium atoms by carbonate. Moreover, under the groundwater conditions present, Ca(2+) binds strongly to uraninite surfaces at structural uranium sites, impacting uranium fate.

Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site.

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. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.

Missense Mutation R338W in ARHGEF9 in a Family with X-linked Intellectual Disability with Variable Macrocephaly and Macro-Orchidism.

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. Although a previous linkage study had mapped the locus to Xq12-q21, this region contained too many candidate genes to be analyzed using conventional approaches. However, X-chromosome exome sequencing, bioinformatics analysis and segregation analysis revealed a novel missense mutation (c.1012C>T; p.R338W) in ARHGEF9. This gene encodes collybistin (CB), a neuronal GDP-GTP exchange factor previously implicated in several cases of XLID, as well as clustering of gephyrin and GABAA receptors at inhibitory synapses. Molecular modeling of the CB R338W substitution revealed that this change results in the substitution of a long electropositive side-chain with a large non-charged hydrophobic side-chain. The R338W change is predicted to result in clashes with adjacent amino acids (K363 and N335) and disruption of electrostatic potential and local folding of the PH domain, which is known to bind phosphatidylinositol-3-phosphate (PI3P/PtdIns-3-P). Consistent with this finding, functional assays revealed that recombinant CB CB2SH3- (R338W) was deficient in PI3P binding and was not able to translocate EGFP-gephyrin to submembrane microaggregates in an in vitro clustering assay. Taken together, these results suggest that the R338W mutation in ARHGEF9 is the underlying cause of NS-XLID in this family.

Novel Missense Mutation A789V in IQSEC2 Underlies X-Linked Intellectual Disability in the MRX78 Family.

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. We report the resolution of MRX78, a large family with six affected males and seven affected females, showing X-linked inheritance. Although a previous linkage study had mapped the locus to the short arm of chromosome X (Xp11.4-p11.23), this region contained too many candidate genes to be analyzed using conventional approaches. However, our X-chromosome exome resequencing, bioinformatics analysis and inheritance testing revealed a missense mutation (c.C2366T, p.A789V) in IQSEC2, encoding a neuronal GDP-GTP exchange factor for Arf family GTPases (ArfGEF) previously implicated in XLID. Molecular modeling of IQSEC2 revealed that the A789V substitution results in the insertion of a larger side-chain into a hydrophobic pocket in the catalytic Sec7 domain of IQSEC2. The A789V change is predicted to result in numerous clashes with adjacent amino acids and disruption of local folding of the Sec7 domain. Consistent with this finding, functional assays revealed that recombinant IQSEC2(A789V) was not able to catalyze GDP-GTP exchange on Arf6 as efficiently as wild-type IQSEC2. Taken together, these results strongly suggest that the A789V mutation in IQSEC2 is the underlying cause of XLID in the MRX78 family.

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.

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. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.