Optical properties of current carrying molecular wires

We consider several fundamental optical phenomena involving single molecules in biased metal-molecule-metal junctions. The molecule is represented by its highest occupied and lowest unoccupied molecular orbitals, and the analysis involves the simultaneous consideration of three coupled fluxes: the electronic current through the molecule, energy flow between the molecule and electron-hole excitations in the leads and the incident and/or emitted photon flux. Using a unified theoretical approach based on the non-equilibrium Green function method we derive expressions for the absorption lineshape (not an observable but a ueful reference for considering yields of other optical processes) and for the current induced molecular emission in such junctions. We also consider conditions under which resonance radiation can induce electronic current in an unbiased junction. We find that current driven molecular emission and resonant light induced electronic currents in single molecule junctions can be of observable magnitude under appropriate realizable conditions. In particular, light induced current should be observed in junctions involving molecular bridges that are characterized by strong charge transfer optical transitions. For observing current induced molecular emission we find that in addition to the familiar need to control the damping of molecular excitations into the metal substrate the phenomenon is also sensitive to the way in which the potential bias si distributed on the junction.Comment: 56 pages, 8 figures; submitted to JC

Mapping isoprene emissions over North America using formaldehyde column observations from space

We present a methodology for deriving emissions of volatile organic compounds (VOC) using space-based column observations of formaldehyde (HCHO) and apply it to data from the Global Ozone Monitoring Experiment (GOME) satellite instrument over North America during July 1996. The HCHO column is related to local VOC emissions, with a spatial smearing that increases with the VOC lifetime. Isoprene is the dominant HCHO precursor over North America in summer, and its lifetime (≃1 hour) is sufficiently short that the smearing can be neglected. We use the Goddard Earth Observing System global 3-D model of tropospheric chemistry (GEOS-CHEM) to derive the relationship between isoprene emissions and HCHO columns over North America and use these relationships to convert the GOME HCHO columns to isoprene emissions. We also use the GEOS-CHEM model as an intermediary to validate the GOME HCHO column measurements by comparison with in situ observations. The GEOS-CHEM model including the Global Emissions Inventory Activity (GEIA) isoprene emission inventory provides a good simulation of both the GOME data (r2 = 0.69, n = 756, bias = +11%) and the in situ summertime HCHO measurements over North America (r2 = 0.47, n = 10, bias = −3%). The GOME observations show high values over regions of known high isoprene emissions and a day-to-day variability that is consistent with the temperature dependence of isoprene emission. Isoprene emissions inferred from the GOME data are 20% less than GEIA on average over North America and twice those from the U.S. EPA Biogenic Emissions Inventory System (BEIS2) inventory. The GOME isoprene inventory when implemented in the GEOS-CHEM model provides a better simulation of the HCHO in situ measurements than either GEIA or BEIS2 (r2 = 0.71, n = 10, bias = −10%)

Photonic mode density effects on single-molecule fluorescence blinking

We investigated the influence of the photonic mode density (PMD) on the triplet dynamics of individual chromophores on a dielectric interface by comparing their response in the presence and absence of a nearby gold film. Lifetimes of the excited singlet state were evaluated in ordet to measure directly the PMD at the molecules position. Triplet state lifetimes were simultaneously determined by statistical analysis of the detection time of the fluorescence photons. The observed singlet decay rates are in agreement with the predicted PMD for molecules with different orientations. The triplet decay rate is modified in a fashion correlated to the singlet decay rate. These results show that PMD engineering can lead to an important suppression of the fluorescence, introducing a novel aspect of the physical mechanism to enhance fluorescence intensity in PMD-enhancing systems such as plasmonic devices

Robust Inference of Kinase Activity Using Functional Networks

Mass spectrometry enables high-throughput screening of phosphoproteins across a broad range of biological contexts. When complemented by computational algorithms, phospho-proteomic data allows the inference of kinase activity, facilitating the identification of dysregulated kinases in various diseases including cancer, Alzheimer’s disease and Parkinson’s disease. To enhance the reliability of kinase activity inference, we present a network-based framework, RoKAI, that integrates various sources of functional information to capture coordinated changes in signaling. Through computational experiments, we show that phosphorylation of sites in the functional neighborhood of a kinase are significantly predictive of its activity. The incorporation of this knowledge in RoKAI consistently enhances the accuracy of kinase activity inference methods while making them more robust to missing annotations and quantifications. This enables the identification of understudied kinases and will likely lead to the development of novel kinase inhibitors for targeted therapy of many diseases. RoKAI is available as web-based tool at http://rokai.io

A comparison of spectrophotometric and denuder based approaches for the determination of gaseous molecular iodine

The presence of molecular iodine in the atmosphere is thought to have implications for both climate and human nutritional health, but measurement of the gas at low concentrations requires technically demanding techniques that are not widely accessible. Here, amylose coated denuder tubes and solvent traps coupled with spectrophotometric detection are evaluated and compared as relatively cheap and straightforward methods to measure gaseous molecular iodine at environmentally relevant concentrations. Denuder tubes were found to give unacceptably low and highly variable recoveries of molecular iodine from a test gas source, with values ranging from 1 to 62%. Blank concentrations were also high, being equivalent to a gas phase concentration of 5 pptv under typical operating conditions. Ethanol and hexane solvent traps gave much better performance. Optimisation of the hexane solvent trap method gave 100% recovery and an atmospheric limit of detection of 70 pptv, which is within the range of concentrations observed in the coastal marine atmosphere

Characterization of the OCO-2 instrument line shape functions using on-orbit solar measurements

Accurately characterizing the instrument line shape (ILS) of the Orbiting Carbon Observatory-2 (OCO-2) is challenging and highly important due to its high spectral resolution and requirement for retrieval accuracy (0. 25 %) compared to previous spaceborne grating spectrometers. On-orbit ILS functions for all three bands of the OCO-2 instrument have been derived using its frequent solar measurements and high-resolution solar reference spectra. The solar reference spectrum generated from the 2016 version of the Total Carbon Column Observing Network (TCCON) solar line list shows significant improvements in the fitting residual compared to the solar reference spectrum currently used in the version 7 Level 2 algorithm in the O₂ A band. The analytical functions used to represent the ILS of previous grating spectrometers are found to be inadequate for the OCO-2 ILS. Particularly, the hybrid Gaussian and super-Gaussian functions may introduce spurious variations, up to 5 % of the ILS width, depending on the spectral sampling position, when there is a spectral undersampling. Fitting a homogeneous stretch of the preflight ILS together with the relative widening of the wings of the ILS is insensitive to the sampling grid position and accurately captures the variation of ILS in the O₂ A band between decontamination events. These temporal changes of ILS may explain the spurious signals observed in the solar-induced fluorescence retrieval in barren areas

Respiratory muscle deoxygenation during exercise in patients with heart failure demonstrated with near-infrared spectroscopy

AbstractExertional dyspnea in patients with heart failure may be due, in part, to respiratory muscle underperfusion. Near-infrared spectroscopy is a new technique that permits noninvasive assessment of skeletal muscle oxygenation by monitoring changes in nearinfrared light absorption. With use of near-infrared spectroscopy, serratus anterior muscle oxygenation during maximal bicycle exercise was compared in 10 patients with heart failure (ejection fraction 16 ± 5%) and 7 age-matched normal subjects. Oxygen consumption (VO2), minute ventilation (VE) and arterial saturation were also measured. Changes in difference in absorption between 760 and 800 nm, expressed in arbitrary units, were used to detect muscle deoxygenation.Minimal change in this difference in absorption occurred in normal subjects during exercise, whereas patients with heart failure exhibited progressive changes throughout exercise consistent with respiratory muscle deoxygenation (peak exercise: normal 3 ± 6, heart failure 12 ± 4 near-infrared arbitrary units, p < 0.001). At comparable work loads patiente with heart failure had significantly greater minute ventilation and respiratory rate but similar tidal volume when contrasted with normal subjects. However, at peak exercise normal subjects achieved significantly greater minute ventilation and tidal volume with a comparable respiratory rate. No significant arterial desaturation occurred during exercise in either group.These findings indicate that respiratory muscle deoxygenation occurs in patients with heart failure during exercise. This deoxygenation may contribute to the exertional dyspnea experienced by such patients

Urinary Protein Profiles in a Rat Model for Diabetic Complications

Diabetes mellitus is estimated to affect ∼24 million people in the United States and more than 150 million people worldwide. There are numerous end organ complications of diabetes, the onset of which can be delayed by early diagnosis and treatment. Although assays for diabetes are well founded, tests for its complications lack sufficient specificity and sensitivity to adequately guide these treatment options. In our study, we employed a streptozotocin- induced rat model of diabetes to determine changes in urinary protein profiles that occur during the initial response to the attendant hyperglycemia (e.g. the first two months) with the goal of developing a reliable and reproducible method of analyzing multiple urine samples as well as providing clues to early markers of disease progression. After filtration and buffer exchange, urinary proteins were digested with a specific protease, and the relative amounts of several thousand peptides were compared across rat urine samples representing various times after administration of drug or sham control. Extensive data analysis, including imputation of missing values and normalization of all data was followed by ANOVA analysis to discover peptides that were significantly changing as a function of time, treatment and interaction of the two variables. The data demonstrated significant differences in protein abundance in urine before observable pathophysiological changes occur in this animal model and as function of the measured variables. These included decreases in relative abundance of major urinary protein precursor and increases in pro-alpha collagen, the expression of which is known to be regulated by circulating levels of insulin and/or glucose. Peptides from these proteins represent potential biomarkers, which can be used to stage urogenital complications from diabetes. The expression changes of a pro-alpha 1 collagen peptide was also confirmed via selected reaction monitoring

New retrieval of BrO from SCIAMACHY limb: an estimate of the stratospheric bromine loading during April 2008

We present a new retrieval of stratospheric BrO (bromine monoxide) from channel 2 SCIAMACHY (SCanning Imaging Absorption spectrometer for Atmospheric CHartographY) limb observations. Retrievals are shown to agree with independent balloon observations to within one standard deviation of the retrieval noise. We retrieve BrO profiles for all of April 2008, and apply simulated [BrO]/[Br_y] (bromine monoxide : stratospheric inorganic bromine) ratios to estimate the stratospheric Br_y loading. We find 23.5 ± 6 ppt Br, suggesting 7 ppt Br from short-lived bromocarbons to be at the high end of the current best estimate (3–8 ppt). The 6 ppt Br uncertainty estimate is dominated by the 21% uncertainty in the simulated [BrO] / [Br_y] ratio due to propagation of errors from the underlying chemical kinetics

Key Inflammatory Pathway Activations in the MCI Stage of Alzheimer’s disease

Objective: To determine the key inflammatory pathways that are activated in the peripheral and CNS compartments at the mild cognitive impairment (MCI) stage of Alzheimer’s disease (AD). Methods: A cross-sectional study of patients with clinical and biomarker characteristics consistent with MCI-AD in a discovery cohort, with replication in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. Inflammatory analytes were measured in the CSF and plasma with the same validated multiplex analyte platform in both cohorts and correlated with AD biomarkers (CSF Aβ42, total tau (t-tau), phosphorylated tau (p-tau) to identify key inflammatory pathway activations. The pathways were additionally validated by evaluating genes related to all analytes in coexpression networks of brain tissue transcriptome from an autopsy confirmed AD cohort to interrogate if the same pathway activations were conserved in the brain tissue gene modules. Results: Analytes of the tumor necrosis factor (TNF) signaling pathway (KEGG ID:4668) in the CSF and plasma best correlated with CSF t-tau and p-tau levels, and analytes of the complement and coagulation pathway (KEGG ID:4610) best correlated with CSF Aβ42 levels. The top inflammatory signaling pathways of significance were conserved in the peripheral and the CNS compartments. They were also confirmed to be enriched in AD brain transcriptome gene clusters. Interpretation: A cell-protective rather than a proinflammatory analyte profile predominates in the CSF in relation to neurodegeneration markers among MCI-AD patients. Analytes from the TNF signaling and the complement and coagulation pathways are relevant in evaluating disease severity at the MCI stage of AD