Comparison of source-location algorithms for atmospheric samplers.

Numerous algorithms have been developed to determine the source characteristics for an atmospheric radionuclide release, e.g., (Bieringer et al., 2017). This study compares three models that have been applied to the data collected by the International Monitoring System operated by the Comprehensive Nuclear-Test-Ban Treaty Organization Preparatory Commission to estimate source event parameters. Each model uses a different approach to estimate the parameters. A deterministic model uses a possible source region (PSR) approach (Ringbom et al., 2014) that is based on the correlation between predicted and measured sample values. A model (now called BAYEST) developed at Pacific Northwest National Laboratory uses a Bayesian formulation (Eslinger et al., 2019, 2020; Eslinger and Schrom, 2016). The FREAR model uses a different Bayesian formulation (De Meutter and Hoffman, 2020; De Meutter et al., 2021a, 2021b). The performance of the three source-location models is evaluated with 100 synthetic release cases for the single xenon isotope, 133Xe. The release cases resulted in detections in a fictitious network with 120 noble gas samplers. All three source-location models use the same sampling data. The two Bayesian models yield more accurate location estimates than the deterministic PSR model, with FREAR having slightly better location performance than BAYEST. Samplers with collection periods of 3, 6, 8, 12, and 24-h were used. Results from BAYEST show that location accuracy improves with each reduction in sample collection length. The BAYEST model is slightly better for estimating the start time of the release. The PSR model has about the same spread in start times as the FREAR model, but the PSR results have a better average start time. The Bayesian source-location algorithms give more accurate results than the PSR approach, and provide release magnitude estimates, while the base PSR model does not estimate the release magnitude. This investigation demonstrates that a reasonably dense sampling grid will sometimes yield poor location and time estimates regardless of the model. The poor estimates generally coincide with cases where there is a much larger distance between the release point and the first detecting sampler than the average sampler spacing.

Nuclear explosion monitoring network design considerations.

Design of an efficient monitoring network requires information on the type and size of releases to be detected, the accuracy and reliability of the measuring equipment, and the desired network performance. This work provides a scientific basis for optimizing or minimizing networks of 133Xe samplers to achieve a desired performance level for different levels of release. The approach of this work varies the density of sampling locations to find optimal location subsets, and to explore the properties of variations of those subsets - how crucial is a specific subset; are substitutions problematic? The choice of possible station locations is arbitrary but constrained to some extent by the location of islands, land masses, difficult topography (mountains, etc.) and the places where infrastructure exists to run and support a sampler. Performance is evaluated using hypothetical releases and atmospheric transport models that cover an entire year. Three network performance metrics are calculated: the probability of detecting the releases, the expected number of stations to detect the releases, and the expected number of samples that detect the releases. The quantitative measures support picking optimal or near-optimal network of a specific station density. If a detection probability of 90% (high) was desired for a design basis release of 1014 Bq (1% of 133Xe production from a 1 kt explosion), then a very high density would be required using today's sampling and measurement technology. If the design basis release were raised to 1015 Bq, then the station density could be lowered by a factor of 3. To achieve a location goal of three station detections on average, posited here for the first time, would also require very high station density for a release of 1014 Bq.

An open database of computed bulk ternary transition metal dichalcogenides.

We present a dataset of structural relaxations of bulk ternary transition metal dichalcogenides (TMDs) computed via plane-wave density functional theory (DFT). We examined combinations of up to two chalcogenides with seven transition metals from groups 4-6 in octahedral (1T) or trigonal prismatic (2H) coordination. The full dataset consists of 672 unique stoichiometries, with a total of 50,337 individual configurations generated during structural relaxation. Our motivations for building this dataset are (1) to develop a training set for the generation of machine and deep learning models and (2) to obtain structural minima over a range of stoichiometries to support future electronic analyses. We provide the dataset as individual VASP xml files as well as all configurations encountered during relaxations collated into an ASE database with the corresponding total energy and atomic forces. In this report, we discuss the dataset in more detail and highlight interesting structural and electronic features of the relaxed structures.

An experimental, computational, and uncertainty analysis study of the rates of iodoalkane trapping by DABCO in solution phase organic media.

NMR spectroscopy was used to measure the rates of the first and second substitution reactions between iodoalkane (R = Me, 1-butyl) and DABCO in methanol, acetonitrile and DMSO. Most of the reactions were recorded at three different temperatures, which permitted calculation of the activation parameters from Eyring and Arrhenius plots. Additionally, the reaction rate and heat of reaction for 1-iodobutane + DABCO in acetonitrile and DMSO were also measured using calorimetry. To help interpret experimental results, ab initio calculations were performed on the reactant, product, and transition state entities to understand structures, reaction enthalpies and activation parameters. Markov chain Monte Carlo statistical sampling was used to determine a distribution of kinetic rates with respect to the uncertainties in measured concentrations and correlations between parameters imposed by a kinetics model. The reactions with 1-iodobutane are found to be slower in all cases compared to reactions under similar conditions for iodomethane. This is due to steric crowding around the reaction centre for the larger butyl group compared to methyl which results in a larger activation energy for the reaction.

Optimization of Thermal Conductance at Interfaces Using Machine Learning Algorithms.

Optimization of thermal transport across the interface of two different materials is critical to micro-/nanoscale electronic, photonic, and phononic devices. Although several examples of compositional intermixing at the interfaces having a positive effect on interfacial thermal conductance (ITC) have been reported, an optimum arrangement has not yet been determined because of the large number of potential atomic configurations and the significant computational cost of evaluation. On the other hand, computation-driven materials design efforts are rising in popularity and importance. Yet, the scalability and transferability of machine learning models remain as challenges in creating a complete pipeline for the simulation and analysis of large molecular systems. In this work we present a scalable Bayesian optimization framework, which leverages dynamic spawning of jobs through the Message Passing Interface (MPI) to run multiple parallel molecular dynamics simulations within a parent MPI job to optimize heat transfer at the silicon and aluminum (Si/Al) interface. We found a maximum of 50% increase in the ITC when introducing a two-layer intermixed region that consists of a higher percentage of Si. Because of the random nature of the intermixing, the magnitude of increase in the ITC varies. We observed that both homogeneity/heterogeneity of the intermixing and the intrinsic stochastic nature of molecular dynamics simulations account for the variance in ITC.

Enabling probabilistic retrospective transport modeling for accurate source detection.

Predicting source or background radionuclide emissions is limited by the effort needed to run gas/aerosol atmospheric transport models (ATMs). A high-performance surrogate model is developed for the HYSPLIT4 (NOAA) ATM to accelerate transport simulation through model reduction, code optimization, and improved scaling on high performance computing systems. The surrogate model parameters are a grid of short-duration transport simulations stored offline. The surrogate model then predicts the path of a plume of radionuclide particles emitted from a source, or the field of sources which may have contributed to a detected signal, more efficiently than direct simulation by HYSPLIT4. Termed the Atmospheric Transport Model Surrogate (ATaMS), this suite of capabilities forms a basis to accelerate workflows for probabilistic source prediction and estimation of the radionuclide atmospheric background.

Source term estimation using multiple xenon isotopes in atmospheric samples.

Algorithms that estimate the location and magnitude of an atmospheric release using remotely sampled air concentrations typically involve a single chemical or radioactive isotope. A new Bayesian algorithm is presented that makes discrimination between possible types of releases (e.g., nuclear explosion, nuclear power plant, or medical isotope production facility) an integral part of the analysis for samples that contain multiple isotopes. Algorithm performance is demonstrated using synthetic data and correctly discriminated between most release-type hypotheses, with higher accuracy when data are available on three or more isotopes.

Exploring the challenges of implementing Participatory Action Research in the context of HIV and poverty.

HIV/AIDS is having a devastating impact on South Africa and particularly on poor communities. Empowerment of communities has been identified as an important step towards mitigating the consequences and helping communities to overcome the challenges presented. Participatory Action Research (PAR) has been identified as a useful methodology for the purpose of facilitating empowerment. This study explores the challenges involved in implementing PAR in the context of HIV/AIDS and poverty. In this article, the author describes a PAR project that took place in 2003/ 2004 with a group of five Xhosa speaking people living with HIV/AIDS in Masiphumelele, Cape Town. The aims of the study were to: 1. Create an opportunity for the participants to engage in a participatory process aimed at self-awareness and empowerment. 2. To record and analyse this process with the intention of producing insight into the use of PAR in the context of poverty and HIV/AIDS and to identify the challenges involved. The findings of this study highlight some important insights into the process of engaging people in the PAR process and the experiences of HIV positive people living in the context of poverty. The study explores the challenges involved in the process of empowerment and examines the process of "transferring" power and control from the researcher to the participants. Challenges were uncovered both from the point of view of the researcher who had to "let go of control" and participants who had to take on control. Participants struggled with issues of low self-efficacy and learned helplessness. Fluctuations in health also contributed towards alternating periods of hope and despair and these problems had an impact on their motivation to participate in the study. Lack of motivation to participate is a challenge highlighted in the literature and explored in this study. Participation is necessary for a study of this nature to be of benefit to the community, but unfortunately those most in need were found to be least likely to participate. The study also critically examines the research process that was conducted and highlights the positive and negative contribution of the process towards empowerment. Certain aspects of the research process, including the contracting process, were identified as being problematic as they emphasize the power and control of the researcher rather than the participants. Recommendations for future research include: Promoting participation among the disempowered; the Contracting process and Power relations in PAR.

Peptides for disruption of PKA anchoring.

Adaptor or scaffolding proteins are at the basis of multiprotein complexes that spatially and temporally co-ordinate the propagation and integration of a broad range of cellular events. One class of scaffolding proteins are AKAPs (A-kinase-anchoring proteins). They sequester PKA (protein kinase A) and other signalling molecules including phosphodiesterases, other protein kinases and protein phosphatases to specific subcellular compartments. AKAP-dependent protein-protein interactions play a role in many physiologically relevant processes. For example, AKAP-PKA interactions are essential for the vasopressin-mediated water re-absorption in renal collecting duct principal cells or beta-adrenoceptor-induced increases in cardiac myocyte contractility. Here, we discuss recently developed peptide disruptors of AKAP-PKA interactions. Such peptides are valuable tools to study the relevance of PKA anchoring in cellular processes.

Compartmentalized cAMP signalling regulates vasopressin-mediated water reabsorption by controlling aquaporin-2.

The cAMP/PKA (protein kinase A) signalling pathway is activated by a plethora of stimuli. To facilitate the specificity of a cellular response, signal transduction complexes are formed and segregated to discrete sites (compartmentalization). cAMP/PKA signalling compartments are maintained by AKAPs (A-kinase anchoring proteins) which bind PKA and other signalling proteins, and by PDEs (phosphodiesterases). The latter hydrolyse cAMP and thus limit its diffusion and terminate PKA activity. An example of a cAMP-dependent process requiring compartmentalization of cAMP/PKA signals is arginine-vasopressin-regulated water reabsorption in renal principal cells. A detailed understanding of the protein interactions within a signal transduction complex offers the possibility to design agents influencing PKA binding to a specific AKAP, the targeting of an AKAP or the interactions of AKAPs with other signalling molecules. The ability to specifically modulate selected branches of a signal transduction pathway would greatly advance basic research, and may lead to new drugs suitable for the treatment of diseases caused by dysregulation of anchored PKA signalling (e.g. renal and cardiovascular diseases).

Osmolality and solute composition are strong regulators of AQP2 expression in renal principal cells.

The water permeability of the renal collecting duct is regulated by the insertion of aquaporin-2 (AQP2) into the apical plasma membrane of epithelial (principal) cells. Using primary cultured epithelial cells from the inner medulla of rat kidney (IMCD cells), we show that osmolality and solute composition are potent regulators of AQP2 mRNA and protein synthesis, as well as the classical cAMP-dependent pathway, but do not affect the arginine vasopressin-induced AQP2 shuttle. In the presence of the cAMP analog dibutyryl cAMP (DBcAMP, 500 microM), NaCl and sorbitol, but not urea, evoked a robust increase of AQP2 expression in IMCD cells, with NaCl being far more potent than sorbitol. cAMP-responsive element-binding protein phosphorylation increased with DBcAMP concentrations but was not altered by changes in osmolality. In the rat and human AQP2 promoter, we identified a putative tonicity-responsive element. We conclude that, in addition to the arginine vasopressin/cAMP-signaling cascade, a further pathway activated by elevated effective osmolality (tonicity) is crucial for the expression of AQP2 in IMCD cells, and we suggest that the effect is mediated via the tonicity-responsive element.

Rho inhibits cAMP-induced translocation of aquaporin-2 into the apical membrane of renal cells.

First published August 8, 2001; 10.1152/ajprenal.00091.2001.-We have recently demonstrated that actin depolymerization is a prerequisite for cAMP-dependent translocation of the water channel aquaporin-2 (AQP2) into the apical membrane in AQP2-transfected renal CD8 cells (29). The Rho family of small GTPases, including Cdc42, Rac, and Rho, regulates the actin cytoskeleton. In AQP2-transfected CD8 cells, inhibition of Rho GTPases with Clostridium difficile toxin B or with C. limosum C3 fusion toxin, as well as incubation with the Rho kinase inhibitor, Y-27632, caused actin depolymerization and translocation of AQP2 in the absence of the cAMP-elevating agent forskolin. Both forskolin and C3 fusion toxin-induced AQP2 translocation were associated with a similar increase in the osmotic water permeability coefficient. Expression of constitutively active RhoA induced formation of stress fibers and abolished AQP2 translocation in response to forskolin. Cytochalasin D induced both depolymerization of F-actin and AQP2 translocation, suggesting that depolymerization of F-actin is sufficient to induce AQP2 translocation. Together, these data indicate that Rho inhibits cAMP-dependent translocation of AQP2 into the apical membrane of renal principal cells by controlling the organization of the actin cytoskeleton.

Ht31: the first protein kinase A anchoring protein to integrate protein kinase A and Rho signaling.

In an attempt to isolate protein kinase A anchoring proteins (AKAPs) involved in vasopressin-mediated water reabsorbtion, the complete sequence of the human AKAP Ht31 was determined and a partial cDNA of its rat orthologue (Rt31) was cloned. The Ht31 cDNA includes the estrogen receptor cofactor Brx and the RhoA GDP/GTP exchange factor proto-lymphoid blast crisis (Lbc) sequences. The Ht31 gene was assigned to chromosome 15 (region q24-q25). It encodes Ht31 and the smaller splice variants Brx and proto-Lbc. A protein of the predicted size of Ht31 (309 kDa) was detected in human mammary carcinoma and HeLa cells. Anti-Ht31/Rt31 antibodies immunoprecipitated RhoA from primary cultured rat renal inner medullary collecting duct cells, indicating an interaction between the AKAP and RhoA in vivo. These results suggest that Ht31/Rt31 represent a new type of AKAP, containing both an anchoring and a catalytic domain, which appears to be capable of modulating the activity of an interacting partner. Ht31/Rt31 have the potential to integrate Rho and protein kinase A signaling pathways, and thus, are prime candidates to regulate vasopressin-mediated water reabsorbtion.

Role and identification of protein kinase A anchoring proteins in vasopressin-mediated aquaporin-2 translocation.

The antidiuretic hormone arginine vasopressin (AVP) regulates water reabsorption in renal principal cells by inducing a cAMP/protein kinase A-dependent translocation of water channels [aquaporin-2 (AQP2)] from intracellular vesicles into the apical cell membranes. Using primary cultured rat inner medullary collecting duct (IMCD) cells, it has been shown that AQP2 translocation in response to AVP stimulation occurs only if protein kinase A (PKA) is anchored to PKA anchoring proteins (AKAPs), which are present in various subcellular compartments. The identity of the AKAPs involved has not yet been elucidated. One potential candidate is a new splice variant of AKAP18, namely AKAP18 delta.

Cell volume kinetics of adherent epithelial cells measured by laser scanning reflection microscopy: determination of water permeability changes of renal principal cells.

The water channel aquaporin-2 (AQP2), a key component of the antidiuretic machinery in the kidney, is rapidly regulated by the antidiuretic hormone vasopressin. The hormone exerts its action by inducing a translocation of AQP2 from intracellular vesicles to the cell membrane. This step requires the elevation of intracellular cyclic AMP. We describe here a new method, laser scanning reflection microscopy (LSRM), suitable for determining cellular osmotic water permeability coefficient changes in primary cultured inner medullary collecting duct (IMCD) cells. The recording of vertical-reflection-mode x-z-scan section areas of unstained, living IMCD cells proved useful and valid for the investigation of osmotic water permeability changes. The time-dependent increases of reflection-mode x-z-scan section areas of swelling cells were fitted to a single-exponential equation. The analysis of the time constants of these processes indicates a twofold increase in osmotic water permeability of IMCD cells after treatment of the cells both with forskolin, a cyclic AMP-elevating agent, and with Clostridium difficile toxin B, an inhibitor of Rho proteins that leads to depolymerization of F-actin-containing stress fibers. This indicates that both agents lead to the functional insertion of AQP2 into the cell membrane. Thus, we have established a new functional assay for the study of the regulation of the water permeability at the cellular level.

An inhibitory role of Rho in the vasopressin-mediated translocation of aquaporin-2 into cell membranes of renal principal cells.

Vasopressin regulates water reabsorption in renal collecting duct principal cells by a cAMP-dependent translocation of the water channel aquaporin-2 (AQP2) from intracellular vesicles into the cell membrane. In the present work primary cultured inner medullary collecting duct cells were used to study the role of the proteins of the Rho family in the translocation of AQP2. Clostridium difficile toxin B, which inhibits all members of the Rho family, Clostridium limosum C3 toxin, which inactivates only Rho, and the Rho kinase inhibitor, Y-27632, induced both depolymerization of actin stress fibers and AQP2 translocation in the absence of vasopressin. The data suggest an inhibitory role of Rho in this process, whereby constitutive membrane localization is prevented in resting cells. Expression of constitutively active RhoA induced formation of actin stress fibers and abolished AQP2 translocation in response to elevation of intracellular cAMP, confirming the inhibitory role of Rho. Cytochalasin D induced both depolymerization of the F-actin cytoskeleton and AQP2 translocation, indicating that depolymerization of F-actin is sufficient to induce AQP2 translocation. Thus Rho is likely to control the intracellular localization of AQP2 via regulation of the F-actin cytoskeleton.

Functional rescue of the nephrogenic diabetes insipidus-causing vasopressin V2 receptor mutants G185C and R202C by a second site suppressor mutation.

Mutations in the gene of the G protein-coupled vasopressin V2 receptor (V2 receptor) cause X-linked nephrogenic diabetes insipidus (NDI). Most of the missense mutations on the extracellular face of the receptor introduce additional cysteine residues. Several groups have proposed that these residues might disrupt the conserved disulfide bond of the V2 receptor. To test this hypothesis, we first calculated a structure model of the extracellular receptor domains. The model suggests that the additional cysteine residues may form a second disulfide bond with the free, nonconserved extracellular cysteine residue Cys-195 rather than impairing the conserved bond. To address this question experimentally, we used the NDI-causing mutant receptors G185C and R202C. Their Cys-195 residues were replaced by alanine to eliminate the hypothetical second disulfide bonds. This second site mutation led to functional rescue of both NDI-causing mutant receptors, strongly suggesting that the second disulfide bonds are indeed formed. Furthermore we show that residue Cys-195, which is sensitive to "additional cysteine" mutations, is not conserved among the V2 receptors of other species and that the presence of an uneven number of extracellular cysteine residues, as in the human V2 receptor, is rare among class I G protein-coupled receptors.

Evidence for downregulation of the endothelin-B-receptor by the use of fluorescent endothelin-1 and a fusion protein consisting of the endothelin-B-receptor and the green fluorescent protein.

We generated fusion proteins consisting of the endothelin-B (ET(B))-receptor and the enhanced green fluorescent protein (EGFP) to visualize receptor internalization. In Madin Darby canine kidney (MDCK) clones expressing ET(B)/EGFP fusion proteins, single class high affinity binding sites for [125I]endothelin-1 (ET-1) were found (for two different clones apparent K(D) values were 31 +/- 15 pM and 30 +/- 7 pM). Pretreatment of membranes with GTPgammaS prior to saturation analysis did not alter these values. We also labelled ET-1 with cyanine-dyes (Cy3/ET-1, Cy5/ET-1). In displacement analyses with membranes of MDCK ET(B)/EGFP clones using [125I]ET-1, we found reduced affinity for Cy3/ET-1 and Cy5/ET-1 (about 5- to 10-fold, respectively), but normal efficacy when compared to unlabelled ET-1. Both fluorescent ligands and the ET(B)/EGFP fusion protein were suitable for analysis of receptor trafficking in living cells and cells fixed at different timepoints. Laser scanning microscopy of MDCK ET(B)/EGFP clones incubated with Cy3/ET-1 or Cy5/ET-1 revealed rapid internalization of ligand/receptor complexes, which clustered in large, perinuclear structures (most probably late endosomes). Our data argue against recycling of the ET(B) receptor and favour its targeting to the lysosomal pathway.

The mechanisms of aquaporin control in the renal collecting duct.

The antidiuretic hormone arginine-vasopressin (AVP) regulates water reabsorption in renal collecting duct principal cells. Central to its antidiuretic action in mammals is the exocytotic insertion of the water channel aquaporin-2 (AQP2) from intracellular vesicles into the apical membrane of principal cells, an event initiated by an increase in cAMP and activation of protein kinase A. Water is then reabsorbed from the hypotonic urine of the collecting duct. The water channels aquaporin-3 (AQP3) and aquaporin-4 (AQP4), which are constitutively present in the basolateral membrane, allow the exit of water from the cell into the hypertonic interstitium. Withdrawal of the hormone leads to endocytotic retrieval of AQP2 from the cell membrane. The hormone-induced rapid redistribution between the interior of the cell and the cell membrane establishes the basis for the short term regulation of water permeability. In addition water channels (AQP2 and 3) of principal cells are regulated at the level of expression (long term regulation). This review summarizes the current knowledge on the molecular mechanisms underlying the short and long term regulation of water channels in principal cells. In the first part special emphasis is placed on the proteins involved in short term regulation of AQP2 (SNARE proteins, Rab proteins, cytoskeletal proteins, G proteins, protein kinase A anchoring proteins and endocytotic proteins). In the second part, physiological and pathophysiological stimuli determining the long term regulation are discussed.