Analysis of the potential of near-ground measurements of CO2 and CH4 in London, UK, for the monitoring of city-scale emissions using an atmospheric transport model

Carbon dioxide (CO2) and methane (CH4) mole fractions were measured at four near-ground sites located in and around London during the summer of 2012 with a view to investigating the potential of assimilating such measurements in an atmospheric inversion system for the monitoring of the CO2 and CH4 emissions in the London area. These data were analysed and compared with simulations using a modelling framework suited to building an inversion system: a 2 km horizontal resolution south of England configuration of the transport model CHIMERE driven by European Centre for Medium-Range Weather Forecasts (ECMWF) meteorological forcing, coupled to a 1 km horizontal resolution emission inventory (the UK National Atmospheric Emission Inventory). First comparisons reveal that local sources, which cannot be represented in the model at a 2 km resolution, have a large impact on measurements. We evaluate methods to filter out the impact of some of the other critical sources of discrepancies between the measurements and the model simulation except that of the errors in the emission inventory, which we attempt to isolate. Such a separation of the impact of errors in the emission inventory should make it easier to identify the corrections that should be applied to the inventory. Analysis is supported by observations from meteorological sites around the city and a 3-week period of atmospheric mixing layer height estimations from lidar measurements. The difficulties of modelling the mixing layer depth and thus CO2 and CH4 concentrations during the night, morning and late afternoon lead to focusing on the afternoon period for all further analyses. The discrepancies between observations and model simulations are high for both CO2 and CH4 (i.e. their root mean square (RMS) is between 8 and 12 parts per million (ppm) for CO2 and between 30 and 55 parts per billion (ppb) for CH4 at a given site). By analysing the gradients between the urban sites and a suburban or rural reference site, we are able to decrease the impact of uncertainties in the fluxes and transport outside the London area and in the model domain boundary conditions. We are thus able to better focus attention on the signature of London urban CO2 and CH4 emissions in the atmospheric CO2 and CH4 concentrations. This considerably improves the statistical agreement between the model and observations for CO2 (with model–data RMS discrepancies that are between 3 and 7 ppm) and to a lesser degree for CH4 (with model–data RMS discrepancies that are between 29 and 38 ppb). Between one of the urban sites and either the rural or suburban reference site, selecting the gradients during periods wherein the reference site is upwind of the urban site further decreases the statistics of the discrepancies in general, though not systematically. In a further attempt to focus on the signature of the city anthropogenic emission in the mole fraction measurements, we use a theoretical ratio of gradients of carbon monoxide (CO) to gradients of CO2 from fossil fuel emissions in the London area to diagnose observation-based fossil fuel CO2 gradients, and compare them with the fossil fuel CO2 gradients simulated with CHIMERE. This estimate increases the consistency between the model and the measurements when considering only one of the two urban sites, even though the two sites are relatively close to each other within the city. While this study evaluates and highlights the merit of different approaches for increasing the consistency between the mesoscale model and the near-ground data, and while it manages to decrease the random component of the analysed model–data discrepancies to an extent that should not be prohibitive to extracting the signal from the London urban emissions, large biases, the sign of which depends on the measurement sites, remain in the final model–data discrepancies. Such biases are likely related to local emissions to which the urban near-ground sites are highly sensitive. This questions our current ability to exploit urban near-ground data for the atmospheric inversion of city emissions based on models at spatial resolution coarser than 2 km. Several measurement and modelling concepts are discussed to overcome this challenge

Parameters associated with efficacy of epidural steroid injections in the management of postherpetic neuralgia: the Mayo Clinic experience

Purpose: Thirty percent of patients with postherpetic neuralgia (PHN) receiving conservative treatment report unsatisfactory pain relief. Epidural steroid injections (ESIs) are commonly used as a therapeutic intervention in these patients. In this study, we aimed to determine if there are variables that predict the efficacy of ESI in patients with PHN. Patients and methods: We retrospectively identified patients seen at Mayo Clinic who had PHN and received ESI. From their medical records, we abstracted the demographic variables, concurrent medication use, anatomic approach and medication for ESI, and degree of pain relief at 2 and 12 weeks' postintervention. Results: None of the studied variables were significantly associated with efficacy of ESI in patients with PHN. PHN that began < 11 months before treatment was predictive of a response to ESI at 12 weeks postintervention (positive predictive value, 55%). Patients who reported poor ESI efficacy 2 weeks after the intervention had a 94% chance of still having pain at 12 weeks. Conclusion: For this cohort of patients with PHN being treated with ESI, no demographic characteristics, concurrently used medications, or type of ESI were associated with ESI treatment efficacy at 2 or 12 weeks after the intervention.Open Access JournalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Hyperentangled States

We investigate a new class of entangled states, which we call 'hyperentangled',that have EPR correlations identical to those in the vacuum state of a relativistic quantum field. We show that whenever hyperentangled states exist in any quantum theory, they are dense in its state space. We also give prescriptions for constructing hyperentangled states that involve an arbitrarily large collection of systems.Comment: 23 pages, LaTeX, Submitted to Physical Review

Doxorubicin-Induced Elevated Oxidative Stress and Neurochemical Alterations in Brain and Cognitive Decline: Protection by MESNA and Insights into Mechanisms of Chemotherapy-Induced Cognitive Impairment ( Chemobrain )

Chemotherapy-induced cognitive impairment (CICI) is now widely recognized as a real and too common complication of cancer chemotherapy experienced by an ever-growing number of cancer survivors. Previously, we reported that doxorubicin (Dox), a prototypical reactive oxygen species (ROS)-producing anti-cancer drug, results in oxidation of plasma proteins, including apolipoprotein A-I (ApoA-I) leading to tumor necrosis factor-alpha (TNF-α)-mediated oxidative stress in plasma and brain. We also reported that co-administration of the antioxidant drug, 2-mercaptoethane sulfonate sodium (MESNA), prevents Dox-induced protein oxidation and subsequent TNF-α elevation in plasma. In this study, we measured oxidative stress in both brain and plasma of Dox-treated mice both with and without MESNA. MESNA ameliorated Dox-induced oxidative protein damage in plasma, confirming our prior studies, and in a new finding led to decreased oxidative stress in brain. This study also provides further functional and biochemical evidence of the mechanisms of CICI. Using novel object recognition (NOR), we demonstrated the Dox administration resulted in memory deficits, an effect that was rescued by MESNA. Using hydrogen magnetic resonance imaging spectroscopy (H1-MRS) techniques, we demonstrated that Dox administration led to a dramatic decrease in choline-containing compounds assessed by (Cho)/creatine ratios in the hippocampus in mice. To better elucidate a potential mechanism for this MRS observation, we tested the activities of the phospholipase enzymes known to act on phosphatidylcholine (PtdCho), a key component of phospholipid membranes and a source of choline for the neurotransmitter, acetylcholine (ACh). The activities of both phosphatidylcholine-specific phospholipase C (PC-PLC) and phospholipase D were severely diminished following Dox administration. The activity of PC-PLC was preserved when MESNA was co-administered with Dox; however, PLD activity was not protected. This study is the first to demonstrate the protective effects of MESNA on Dox-related protein oxidation, cognitive decline, phosphocholine (PCho) levels, and PC-PLC activity in brain and suggests novel potential therapeutic targets and strategies to mitigate CICI

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut [version 2; referees: 3 approved]

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software

A Bell Inequality Analog in Quantum Measure Theory

One obtains Bell's inequalities if one posits a hypothetical joint probability distribution, or {\it measure}, whose marginals yield the probabilities produced by the spin measurements in question. The existence of a joint measure is in turn equivalent to a certain causality condition known as ``screening off''. We show that if one assumes, more generally, a joint {\it quantal measure}, or ``decoherence functional'', one obtains instead an analogous inequality weaker by a factor of $\sqrt{2}$. The proof of this ``Tsirel'son inequality'' is geometrical and rests on the possibility of associating a Hilbert space to any strongly positive quantal measure. These results lead both to a {\it question}: ``Does a joint measure follow from some quantal analog of `screening off'?'', and to the {\it observation} that non-contextual hidden variables are viable in histories-based quantum mechanics, even if they are excluded classically.Comment: 38 pages, TeX. Several changes and added comments to bring out the meaning more clearly. Minor rewording and extra acknowledgements, now closer to published versio

Redox Proteomic Identification of HNE-Bound Mitochondrial Proteins in Cardiac Tissues Reveals a Systemic Effect on Energy Metabolism After Doxorubicin Treatment

Doxorubicin (DOX), one of the most effective anticancer drugs, is known to generate progressive cardiac damage, which is due, in part, to DOX-induced reactive oxygen species (ROS). The elevated ROS often induce oxidative protein modifications that result in alteration of protein functions. This study demonstrates that the level of proteins adducted by 4-hydroxy-2-nonenal (HNE), a lipid peroxidation product, is significantly increased in mouse heart mitochondria after DOX treatment. A redox proteomics method involving two-dimensional electrophoresis followed by mass spectrometry and investigation of protein databases identified several HNE-modified mitochondrial proteins, which were verified by HNE-specific immunoprecipitation in cardiac mitochondria from the DOX-treated mice. The majority of the identified proteins are related to mitochondrial energy metabolism. These include proteins in the citric acid cycle and electron transport chain. The enzymatic activities of the HNE-adducted proteins were significantly reduced in DOX-treated mice. Consistent with the decline in the function of the HNE-adducted proteins, the respiratory function of cardiac mitochondria as determined by oxygen consumption rate was also significantly reduced after DOX treatment. Treatment with Mn(III) meso-tetrakis(N-n-butoxyethylpyridinium-2-yl)porphyrin, an SOD mimic, averted the doxorubicin-induced mitochondrial dysfunctions as well as the HNE–protein adductions. Together, the results demonstrate that free radical-mediated alteration of energy metabolism is an important mechanism mediating DOX-induced cardiac injury, suggesting that metabolic intervention may represent a novel approach to preventing cardiac injury after chemotherapy