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This computational research study will compare the specific charge capacity (SCC) between lithium ions inserted into crystallized silicon (c-Si) nanowires with that of sodium ions inserted into amorphous silicon (a-Si) nanowires. It will be demonstrated that the potential energy V(r) within a lithium–silicon nanowire supports a coherent energy state model with discrete electron particles, while the potential energy of a sodium–silicon nanowire will be discovered to be essentially zero, and, thus, the electron current that travels through a sodiated silicon nanowire will be modeled as a free electron with wave-like characteristics. This is due to the vast differences in the electric fields of lithiated and sodiated silicon nanowires, where the electric fields are of the order of 1010 V/m and 10−15 V/m, respectively. The main reason for the great disparity in electric fields is the presence of optical amplification within lithium ions and the absence of this process within sodium ions. It will be shown that optical amplification develops coherent optical interactions, which is the primary reason for the surge of specific charge capacity in the lithiated silicon nanowire. Conversely, the lack of optical amplification is the reason for the incoherent optical interactions within sodium ions, which is the reason for the low presence of SCC in sodiated silicon nanowires.

BackgroundCYP2D6 testing is increasingly used to guide drug therapy and thus, reliable methods are needed to test this complex and polymorphic gene locus. A particular challenge arises from the detection and interpretation of structural variants (SVs) including gene deletions, duplications, and hybrids with the CYP2D7 pseudogene. This study validated the Absolute Q™ platform for digital PCR-based CYP2D6 copy number variation (CNV) determination by comparing results to those obtained with a previously established method using the QX200 platform. In addition, protocols for streamlining CYP2D6 CNV testing were established and validated including the “One-pot” single-step restriction enzyme digestion and a multiplex assay simultaneously targeting the CYP2D6 5′UTR, intron 6, and exon 9 regions.MethodsGenomic DNA (gDNA) samples from Coriell (n = 13) and from blood, saliva, and liver tissue (n = 17) representing 0–6 copies were tested on the Absolute Q and QX200 platforms. Custom TaqMan™ copy number (CN) assays targeting CYP2D6 the 5′UTR, intron 6, and exon 9 regions and a reference gene assay (TERT or RNaseP) were combined for multiplexing by optical channel. In addition, two digestion methods (One-pot digestion and traditional) were assessed. Inconclusive CN values on the Absolute Q were resolved using an alternate reference gene and/or diluting gDNA.ResultsOverall, results between the two platforms and digestions methods were consistent. The “One-pot” digestion method and optically multiplexing up to three CYP2D6 regions yielded consistent result across DNA sample types and diverse SVs, reliably detecting up to 6 gene copies. Rare variation in reference genes were found to interfere with results and interpretation, which were resolved by using a different reference.ConclusionThe Absolute Q produced accurate and reliable CYP2D6 copy number results allowing for a streamlined and economical protocol using One-pot digestion and multiplexing three target regions. Protocols are currently being expanded to other pharmacogenes presenting with SVs/CNVs.

Abstract The DPYD gene encodes dihydropyrimidine dehydrogenase, the rate‐limiting enzyme for the metabolism of fluoropyrimidines 5‐fluorouracil and capecitabine. Genetic variants in DPYD have been associated with altered enzyme activity, therefore accurate detection and interpretation is critical to predict metabolizer status for individualized fluoropyrimidine therapy. The most commonly observed deleterious variation is the causal variant linked to the previously described HapB3 haplotype, c.1129‐5923C>G (rs75017182) in intron 10, which introduces a cryptic splice site. A benign synonymous variant in exon 11, c.1236G>A (rs56038477) is also linked to HapB3 and is commonly used for testing. Previously, these single‐nucleotide polymorphisms (SNPs) have been reported to be in perfect linkage disequilibrium (LD); therefore, c.1236G>A is often utilized as a proxy for the function‐altering intronic variant. Clinical genotyping of DPYD identified a patient who had c.1236G>A, but not c.1129‐5923C>G, suggesting that these two SNPs may not be in perfect LD, as previously assumed. Additional individuals with c.1236G>A, but not c.1129‐5923C>G, were identified in the Children's Mercy Data Warehouse and the All of Us Research Program version 7 cohort substantiating incomplete SNP linkage. Consequently, testing only c.1236G>A can generate false‐positive results in some cases and lead to suboptimal dosing that may negatively impact patient therapy and prospect of survival. Our data show that DPYD genotyping should include the functional variant c.1129‐5923C>G, and not the c.1236G>A proxy, to accurately predict DPD activity.

Abstract Low-temperature thermochronology is a powerful tool for constraining the thermal evolution of rocks and minerals in relation to a breadth of tectonic, geodynamic, landscape evolution, and natural resource formation processes through deep time. However, complexities inherent to these analytical techniques can make interpreting the significance of results challenging, requiring them to be placed in their geological context in 4-dimensions (3D + time). We present a novel tool for the geospatial archival, analysis and dissemination of fission-track and (U-Th)/He data, built as an extension to the open-access AusGeochem platform ( https://ausgeochem.auscope.org.au ) and freely accessible to scientists from around the world. To demonstrate the power of the platform, three regional datasets from Kenya, Australia and the Red Sea are placed in their 4D geological, geochemical, and geographic contexts, revealing insights into the tectono-thermal evolutions of these areas. Beyond facilitating data interpretation, the archival of fission track and (U-Th)/He (meta-)data in relational schemas unlocks future potential for greater integration of thermochronology and numerical geoscience techniques. The power of formatting data to interface with external tools is demonstrated through the integration of GPlates Web Service with AusGeochem, enabling thermochronology data to be readily viewed in their paleogeographic context through deep time from within the platform.

Abstract Northern Malawi's Nyika Plateau is a 3,700 km2 large, highly elevated (∼2,500 m) plateau located at the western margin of the Miocene‐Recent Malawi rift and the confluence of multiple Proterozoic orogenic belts. Neighboring asthenospheric upwelling in the Rungwe Volcanic Province, associated with the active East African Rift, has created similar topographic highs, leading some to speculate that the formation of Nyika could be related. Here, we present new low‐temperature data using apatite fission track, apatite (U‐Th‐Sm)/He and zircon (U‐Th)/He thermochronology to constrain the upper crustal thermal history of the Nyika region since the Devonian. The data suggest that Nyika was an isolated feature since at least the Permo‐Triassic, well before more recent rifting in Malawi, and may have developed as a horst between two large Karoo grabens, the Henga‐Ruhuhu and the North Rukuru to the southeast and northwest, respectively. Similarities between the thermal histories of Nyika and the currently separated Livingstone Plateau to the east allow for the possibility that these may have been connected in a contiguous highland prior to the formation of the intervening Neogene Malawi rift. Thermal history models for exposed Precambrian basement samples adjacent to Nyika, and once buried beneath the neighboring Karoo basins, indicate that up to 3.4 km of Permo‐Triassic section has since been eroded, with samples along the plateau not indicating burial of Karoo‐type sediment at this time. Most recent cooling histories suggest that the plateau surface continued to denude at varying degrees from the Cretaceous and reached near‐surface temperatures in the Late Paleogene‐Neogene.

In the filamentous fungus Neurospora crassa, genes unpaired during meiosis are silenced by a process known as meiotic silencing by unpaired DNA (MSUD). MSUD utilizes common RNA interference (RNAi) proteins, such as Dicer and Argonaute, to target homologous mRNAs for silencing. Previously, we demonstrated that nuclear cap-binding proteins NCBP1 and NCBP2 are involved in MSUD. We report here that SAD-8, a protein similar to human NCBP3, also mediates silencing. Although SAD-8 is not essential for either vegetative or sexual development, it is required for MSUD. SAD-8 localizes predominantly in the nucleus and interacts with both NCBP1 and NCBP2. Similar to NCBP1 and NCBP2, SAD-8 interacts with a component (Argonaute) of the perinuclear meiotic silencing complex (MSC), further implicating the involvement of cap-binding proteins in silencing.

Objective: Hmong individuals represent a unique East Asian subpopulation in whom limited information concerning pharmacogenetic variation exists. The objectives of this study were to comprehensively characterize the highly polymorphic CYP2D6 gene in Hmong, estimate allele and phenotype frequencies and to compare results between two testing platforms.Methods: DNA from 48 self-identified Hmong participants were sequenced using a targeted next-generation sequencing (NGS) panel. Star allele calls were made using Astrolabe, manual inspection of NGS variant calls and confirmatory Sanger sequencing. Structural variation was determined by long-range (XL)-PCR and digital droplet PCR (ddPCR). The consensus diplotypes were subsequently translated into phenotype utilizing the activity score system. Clinical grade pharmacogenetic testing was obtained for 12 of the 48 samples enabling an assessment of concordance between the consensus calls and those determined by clinical testing platforms.Results: A total of 13 CYP2D6 alleles were identified. The most common alleles were CYP2D6*10 and its structural arrangements (37.5%, 36/96) and the *5 gene deletion (13.5%, 13/96). Three novel suballeles (*10.007, *36.004, and *75.002) were also identified. Phenotype frequencies were as follows: ultrarapid metabolizers (4.2%, 2/48), normal metabolizers (41.7%, 20/48) and intermediate metabolizers (52.1%, 25/48); none of the 48 participants were predicted to be poor metabolizers. Concordance of diplotype and phenotype calls between the consensus and clinical testing were 66.7 and 50%, respectively.Conclusion: Our study to explore CYP2D6 genotypes in the Hmong population suggests that this subpopulation is unique regarding CYP2D6 allelic variants; also, a higher portion of Hmong participants (50%) are predicted to have an intermediate metabolizer phenotype for CYP2D6 compared to other East Asians which range between 27 and 44%. Results from different testing methods varied considerably. These preliminary findings underscore the importance of thoroughly interrogating unique subpopulations to accurately predict a patient’s CYP2D6 metabolizer status.

The Oligocene-Recent Red Sea rift is one of the preeminent examples of lithospheric rupture in the recent geological past, forming the basis for many models of how continental breakup occurs and progresses to the formation of new oceanic crust. Utilisation of low-temperature thermochronology in the Red Sea Rift since the 1980s has been key to constraining its spatio-temporal evolution, providing constraints for the propagation of strain and geomorphological development of its margins where datable syn-tectonic strata and/or markers are absent. We review the wealth of published apatite fission track and (U-Th-Sm)/He data from along the Red Sea, affording insights into the Oligocene-Recent thermo-tectonic evolution of the Nubian and Arabian margins. A regional interpolation protocol was employed to synthesise time-temperature reconstructions generated from the mined thermochronology data and burial histories produced from vitrinite reflectance and well data. These cooling-heating maps record a series of pronounced episodes of upper crustal thermal flux related to the development of the Oligocene-Recent Red Sea Rift. Assimilation of these regional thermal history maps with paleogeographic reconstructions and regional magmatic and strain histories provide regional perspectives on the roles of tectonism and geodynamic activity in Red Sea formation and their effects on rift margin development.

Characterizing the structure of riverine fish populations that are patchily distributed and at low densities is often difficult. Due to the wide distribution but low abundance of Spotted Bass, Micropterus punctulatus, throughout the lower Wabash River (LWR), captures from fixed and random sampling designs were compared to assess their performance in determining relative abundance and size structure. The LWR is monitored using both sampling regimes—the Long Term Electrofishing Program monitors community assemblages uses a stratified-random sampling, whereas the Illinois Department of Natural Resources monitors the fish community using a fixed-sampling design. Mean CPUE was significantly higher for fixed site sampling compared to random sites. However, the size structure of Spotted Bass sampled by each design were similar. These results suggest random-sampling designs should be used when monitoring low density populations of fishes in large riverine systems because this method provides the greatest spatial coverage of habitats, evaluates heterogeneity in distribution, and provides a representative measure of abundance throughout an entire aquatic system. In situations where size distribution or temporal trends are the only goal, fixed site sampling would be sufficient.

AbstractIn Neurospora crassaNeurosporaCaenorhabditis elegans

BackgroundThe CYP2D6 gene locus has been extensively studied over decades, yet a portion of variability in CYP2D6 activity cannot be explained by known sequence variations within the gene, copy number variation, or structural rearrangements. It was proposed that rs5758550, located 116 kb downstream of the CYP2D6 gene locus, increases gene expression and thus contributes to variability in CYP2D6 activity. This finding has, however, not been validated. The purpose of the study was to address a major technological barrier, i.e., experimentally linking rs5758550, also referred to as the “enhancer” single-nucleotide polymorphism (SNP), to CYP2D6 haplotypes >100 kb away. To overcome this challenge is essential to ultimately determine the contribution of the “enhancer” SNP to interindividual variability in CYP2D6 activity.MethodsA large ethnically mixed population sample (n=3,162) was computationally phased to determine linkage between the “enhancer” SNP and CYP2D6 haplotypes (or star alleles). To experimentally validate predicted linkages, DropPhase2D6, a digital droplet PCR (ddPCR)-based method was developed. 10X Genomics Linked-Reads were utilized as a proof of concept.ResultsPhasing predicted that the “enhancer” SNP can occur on numerous CYP2D6 haplotypes including CYP2D6*1, *2, *5, and *41 and suggested that linkage is incomplete, i.e., a portion of these alleles do not have the “enhancer” SNP. Phasing also revealed differences among the European and African ancestry data sets regarding the proportion of alleles with and without the “enhancer” SNP. DropPhase2D6 was utilized to confirm or refute the predicted “enhancer” SNP location for individual samples, e.g., of n=3 samples genotyped as *1/*41, rs5758550 was on the *41 allele of two samples and on the *1 allele of one sample. Our findings highlight that the location of the “enhancer” SNP must not be assigned by “default.” Furthermore, linkage between the “enhancer” SNP and CYP2D6 star allele haplotypes was confirmed with 10X Genomics technology.ConclusionsSince the “enhancer” SNP can be present on a portion of normal, decreased, or no function alleles, the phase of the “enhancer” SNP must be considered when investigating the impact of the “enhancer” SNP on CYP2D6 activity.

Atmospheric emissions of carbon tetrachloride (CCl4) are regulated by the Montreal Protocol due to its role as a strong ozone-depleting substance. The molecule has been the subject of recent increased interest as a consequence of the so-called mystery of CCl4, the discrepancy between atmospheric observations and reported production and consumption. Surface measurements of CCl4 atmospheric concentrations have declined at a rate almost 3 times lower than its lifetime-limited rate, suggesting persistent atmospheric emissions despite the ban. In this paper, we study CCl4 vertical and zonal distributions in the upper troposphere and lower stratosphere (including the photolytic loss region, 70–20 hPa), its trend, and its stratospheric lifetime using measurements from the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS), which operated onboard the ENVISAT satellite from 2002 to 2012. Specifically, we use the MIPAS data product generated with Version 7 of the Level 2 algorithm operated by the European Space Agency.The CCl4 zonal means show features typical of long-lived species of anthropogenic origin that are destroyed primarily in the stratosphere, with larger quantities in the troposphere and a monotonic decrease with increasing altitude in the stratosphere. MIPAS CCl4 measurements have been compared with independent measurements from other satellite and balloon-borne remote sounders, showing a good agreement between the different datasets.CCl4 trends are calculated as a function of both latitude and altitude. Negative trends of about −10 to −15 pptv decade−1 (−10 to −30 % decade−1) are found at all latitudes in the upper troposphere–lower stratosphere region, apart from a region in the southern midlatitudes between 50 and 10 hPa where the trend is positive with values around 5–10 pptv decade−1 (15–20 % decade−1). At the lowest altitudes sounded by MIPAS, we find trends consistent with those determined on the basis of long-term ground-based measurements (−10 to −13 pptv decade−1). For higher altitudes, the trend shows a pronounced asymmetry between the Northern and Southern hemispheres, and the magnitude of the decline rate increases with altitude. We use a simplified model assuming tracer–tracer linear correlations to determine CCl4 lifetime in the lower stratosphere. The calculation provides a global average lifetime of 47 (39–61) years, considering CFC-11 as the reference tracer. This value is consistent with the most recent literature result of 44 (36–58) years.

MIPAS thermal limb emission measurements were used to derive vertically resolved profiles of carbon tetrachloride (CCl4). Level-1b data versions MIPAS/5.02 to MIPAS/5.06 were converted into volume mixing ratio profiles using the level-2 processor developed at Karlsruhe Institute of Technology (KIT) Institute of Meteorology and Climate Research (IMK) and Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Astrofísica de Andalucía (IAA). Consideration of peroxyacetyl nitrate (PAN) as an interfering species, which is jointly retrieved, and CO2 line mixing is crucial for reliable retrievals. Parts of the CO2 Q-branch region that overlap with the CCl4 signature were omitted, since large residuals were still found even though line mixing was considered in the forward model. However, the omitted spectral region could be narrowed noticeably when line mixing was accounted for. A new CCl4 spectroscopic data set leads to slightly smaller CCl4 volume mixing ratios. In general, latitude–altitude cross sections show the expected CCl4 features with highest values of around 90 pptv at altitudes at and below the tropical tropopause and values decreasing with altitude and latitude due to stratospheric decomposition. Other patterns, such as subsidence in the polar vortex during winter and early spring, are also visible in the distributions. The decline in CCl4 abundance during the MIPAS Envisat measurement period (July 2002 to April 2012) is clearly reflected in the altitude–latitude cross section of trends estimated from the entire retrieved data set.

In the filamentous fungus Neurospora crassa, cross walls between individual cells are normally incomplete, making the entire fungal network vulnerable to attack by viruses and selfish DNAs. Accordingly, several genome surveillance mechanisms are maintained to help the fungus combat these repetitive elements. One of these defense mechanisms is called meiotic silencing by unpaired DNA (MSUD), which identifies and silences unpaired genes during meiosis. Utilizing common RNA interference (RNAi) proteins, such as Dicer and Argonaute, MSUD targets mRNAs homologous to the unpaired sequence to achieve silencing. In this study, we have identified an additional silencing component, namely the cap-binding complex (CBC). Made up of cap-binding proteins CBP20 and CBP80, CBC associates with the 5′ cap of mRNA transcripts in eukaryotes. The loss of CBC leads to a deficiency in MSUD activity, suggesting its role in mediating silencing. As confirmed in this study, CBC is predominantly nuclear, although it is known to travel in and out of the nucleus to facilitate RNA transport. As seen in animals but not in plants, CBP20’s robust nuclear import depends on CBP80 in Neurospora. CBC interacts with a component (Argonaute) of the perinuclear meiotic silencing complex (MSC), directly linking the two cellular factors.

Changes of atmospheric methane total columns (CH4) since 2005 have been evaluated using Fourier transform infrared (FTIR) solar observations carried out at 10 ground-based sites, affiliated to the Network for Detection of Atmospheric Composition Change (NDACC). From this, we find an increase of atmospheric methane total columns of 0.31 ± 0.03 % year−1 (2σ level of uncertainty) for the 2005–2014 period. Comparisons with in situ methane measurements at both local and global scales show good agreement. We used the GEOS-Chem chemical transport model tagged simulation, which accounts for the contribution of each emission source and one sink in the total methane, simulated over 2005–2012. After regridding according to NDACC vertical layering using a conservative regridding scheme and smoothing by convolving with respective FTIR seasonal averaging kernels, the GEOS-Chem simulation shows an increase of atmospheric methane total columns of 0.35 ± 0.03 % year−1 between 2005 and 2012, which is in agreement with NDACC measurements over the same time period (0.30 ± 0.04 % year−1, averaged over 10 stations). Analysis of the GEOS-Chem-tagged simulation allows us to quantify the contribution of each tracer to the global methane change since 2005. We find that natural sources such as wetlands and biomass burning contribute to the interannual variability of methane. However, anthropogenic emissions, such as coal mining, and gas and oil transport and exploration, which are mainly emitted in the Northern Hemisphere and act as secondary contributors to the global budget of methane, have played a major role in the increase of atmospheric methane observed since 2005. Based on the GEOS-Chem-tagged simulation, we discuss possible cause(s) for the increase of methane since 2005, which is still unexplained.

Background Identifying associations between serum metabolites and visceral adipose tissue (VAT) could provide novel biomarkers of VAT and insights into the pathogenesis of obesity‐related diseases. We aimed to discover and replicate metabolites reflecting pathways related to VAT. Methods and Results Associations between fasting serum metabolites and VAT area (by computed tomography or magnetic resonance imaging) were assessed with cross‐sectional linear regression of individual‐level data from participants in MESA (Multi‐Ethnic Study of Atherosclerosis; discovery, N=1103) and the NEO (Netherlands Epidemiology of Obesity) study (replication, N=2537). Untargeted 1H nuclear magnetic resonance metabolomics profiling of serum was performed in MESA, and metabolites were replicated in the NEO study using targeted 1H nuclear magnetic resonance spectroscopy. A total of 30 590 metabolomic spectral variables were evaluated. After adjustment for age, sex, race/ethnicity, socioeconomic status, smoking, physical activity, glucose/lipid‐lowering medication, and body mass index, 2104 variables representing 24 nonlipid and 49 lipid/lipoprotein subclass metabolites remained significantly associated with VAT (P=4.88×10−20–1.16×10−3). These included conventional metabolites, amino acids, acetylglycoproteins, intermediates of glucose and hepatic metabolism, organic acids, and subclasses of apolipoproteins, cholesterol, phospholipids, and triglycerides. Metabolites mapped to 31 biochemical pathways, including amino acid substrate use/metabolism and glycolysis/gluconeogenesis. In the replication cohort, acetylglycoproteins, branched‐chain amino acids, lactate, glutamine (inversely), and atherogenic lipids remained associated with VAT (P=1.90×10−35–8.46×10−7), with most associations remaining after additional adjustment for surrogates of VAT (glucose level, waist circumference, and serum triglycerides), reflecting novel independent associations. Conclusions We identified and replicated a metabolite panel associated with VAT in 2 community‐based cohorts. These findings persisted after adjustment for body mass index and appear to define a metabolic signature of visceral adiposity.

Profiles of CFC-11 (CCl3F) and CFC-12 (CCl2F2) of the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) aboard the European satellite Envisat have been retrieved from versions MIPAS/4.61 to MIPAS/4.62 and MIPAS/5.02 to MIPAS/5.06 level-1b data using the scientific level-2 processor run by Karlsruhe Institute of Technology (KIT), Institute of Meteorology and Climate Research (IMK) and Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Astrofísica de Andalucía (IAA). These profiles have been compared to measurements taken by the balloon-borne cryosampler, Mark IV (MkIV) and MIPAS-Balloon (MIPAS-B), the airborne MIPAS-STRatospheric aircraft (MIPAS-STR), the satellite-borne Atmospheric Chemistry Experiment Fourier transform spectrometer (ACE-FTS) and the High Resolution Dynamic Limb Sounder (HIRDLS), as well as the ground-based Halocarbon and other Atmospheric Trace Species (HATS) network for the reduced spectral resolution period (RR: January 2005–April 2012) of MIPAS. ACE-FTS, MkIV and HATS also provide measurements during the high spectral resolution period (full resolution, FR: July 2002–March 2004) and were used to validate MIPAS CFC-11 and CFC-12 products during that time, as well as profiles from the Improved Limb Atmospheric Spectrometer, ILAS-II. In general, we find that MIPAS shows slightly higher values for CFC-11 at the lower end of the profiles (below ∼ 15 km) and in a comparison of HATS ground-based data and MIPAS measurements at 3 km below the tropopause. Differences range from approximately 10 to 50 pptv ( ∼ 5–20 %) during the RR period. In general, differences are slightly smaller for the FR period. An indication of a slight high bias at the lower end of the profile exists for CFC-12 as well, but this bias is far less pronounced than for CFC-11 and is not as obvious in the relative differences between MIPAS and any of the comparison instruments. Differences at the lower end of the profile (below ∼ 15 km) and in the comparison of HATS and MIPAS measurements taken at 3 km below the tropopause mainly stay within 10–50 pptv (corresponding to ∼ 2–10 % for CFC-12) for the RR and the FR period. Between ∼ 15 and 30 km, most comparisons agree within 10–20 pptv (10–20 %), apart from ILAS-II, which shows large differences above ∼ 17 km. Overall, relative differences are usually smaller for CFC-12 than for CFC-11. For both species – CFC-11 and CFC-12 – we find that differences at the lower end of the profile tend to be larger at higher latitudes than in tropical and subtropical regions. In addition, MIPAS profiles have a maximum in their mixing ratio around the tropopause, which is most obvious in tropical mean profiles. Comparisons of the standard deviation in a quiescent atmosphere (polar summer) show that only the CFC-12 FR error budget can fully explain the observed variability, while for the other products (CFC-11 FR and RR and CFC-12 RR) only two-thirds to three-quarters can be explained. Investigations regarding the temporal stability show very small negative drifts in MIPAS CFC-11 measurements. These instrument drifts vary between ∼ 1 and 3 % decade−1. For CFC-12, the drifts are also negative and close to zero up to ∼ 30 km. Above that altitude, larger drifts of up to ∼ 50 % decade−1 appear which are negative up to ∼ 35 km and positive, but of a similar magnitude, above.

Ex vivo heart perfusion systems, allowing continuous perfusion of the coronary vasculature, have recently been introduced to limit ischemic time of donor hearts prior to transplantation. Hearts are, however, perfused in an unloaded manner (via the aorta) and therefore, cardiac contractile function cannot be reliably evaluated.We aim to develop a ventricular loading device that enables monitoring of myocardial function in an ex vivo perfusion system. In this initial study, was to develop a prototype for rat experimentation.We designed a device consisting of a ventricular balloon and a reservoir balloon, connected through an electronic check valve, which opens and closes in coordination with changes in ventricular pressure. All balloons were produced in our laboratory and their properties, particularly pressure-volume relationships, were characterized. We developed a mock ventricle in vitro test system to evaluate the device, which was ultimately tested in ex vivo perfused rat hearts.Balloon production was consistent and balloon properties were maintained over time and with use on the device. Results from in vitro and ex vivo experiments show that the device functions appropriately; hemodynamic function can be measured and compares well to measurements made in an isolated, working (loaded) rat heart preparation.Our cardiac loading device appears to reliably allow measurement of several left ventricular hemodynamic parameters and provides the opportunity to control ventricular load.

While global stratospheric O3 has begun to recover, there are localized regions where O3 has decreased since 1991. Specifically, we use measurements from the Halogen Occultation Experiment (HALOE) for the period 1991–2005 and the NASA Aura Microwave Limb Sounder (MLS) for the period 2004–2013 to demonstrate a significant decrease in O3 near ~ 10 hPa in the tropics. O3 in this region is very sensitive to variations in NOy, and the observed decrease can be understood as a spatially localized, yet long-term increase in NOy. In turn, using data from MLS and from the Atmospheric Chemistry Experiment (ACE), we show that the NOy variations are caused by decreases in N2O which are likely linked to long-term variations in dynamics. To illustrate how variations in dynamics can affect N2O and O3, we show that by decreasing the upwelling in the tropics, more of the N2O can photodissociate with a concomitant increase in NOy production (via N2O + O(1D) → 2NO) at 10 hPa. Ultimately, this can cause an O3 decrease of the observed magnitude.

The Total Carbon Column Observing Network (TCCON) is a global ground-based network of Fourier transform spectrometers that produce precise measurements of column-averaged dry-air mole fractions of atmospheric methane (CH4). Temporal variability in the total column of CH4 due to stratospheric dynamics obscures fluctuations and trends driven by tropospheric transport and local surface fluxes that are critical for understanding CH4 sources and sinks. We reduce the contribution of stratospheric variability from the total column average by subtracting an estimate of the stratospheric CH4 derived from simultaneous measurements of hydrogen fluoride (HF). HF provides a proxy for stratospheric CH4 because it is strongly correlated to CH4 in the stratosphere, has an accurately known tropospheric abundance (of zero), and is measured at most TCCON stations. The stratospheric partial column of CH4 is calculated as a function of the zonal and annual trends in the relationship between CH4 and HF in the stratosphere, which we determine from ACE-FTS satellite data. We also explicitly take into account the CH4 column averaging kernel to estimate the contribution of stratospheric CH4 to the total column. The resulting tropospheric CH4 columns are consistent with in situ aircraft measurements and augment existing observations in the troposphere.

Fluorine-containing species can be extremely effective atmospheric greenhouse gases. We present fluorine budgets using organic and inorganic species retrieved by the ACE-FTS satellite instrument supplemented with output from the SLIMCAT 3-D chemical transport model. The budgets are calculated between 2004 and 2009 for a number of latitude bands: 70–30° N, 30–00° N, 00° N–30° S, and 30–70° S. At lower altitudes total fluorine profiles are dominated by the contribution from CFC-12, up to an altitude of 20 km in the extra-tropics and 29 km in the tropics; above these altitudes the profiles are dominated by hydrogen fluoride (HF). Our data show that total fluorine profiles at all locations have a negative slope with altitude, providing evidence that overall fluorine emissions (measured by their F content) have been increasing with time. Total stratospheric fluorine is increasing at a similar rate in the tropics: 32.5 ± 4.9 ppt yr−1 (1.31 ± 0.20% per year) in the Northern Hemisphere (NH) and 29.8 ± 5.3 ppt yr−1 (1.21 ± 0.22% per year) in the Southern Hemisphere (SH). Extra-tropical total stratospheric fluorine is also increasing at a similar rate in both the NH and SH: 28.3 ± 2.7 ppt per year (1.12 ± 0.11% per year) in the NH and 24.3 ± 3.1 ppt per year (0.96 ± 0.12% per year) in the SH. The calculation of radiative efficiency-weighted total fluorine allows the changes in radiative forcing between 2004 and 2009 to be calculated. These results show an increase in radiative forcing of between 0.23 ± 0.11% per year and 0.45 ± 0.11% per year, due to the increase in fluorine-containing species during this time. The decreasing trends in the mixing ratios of halons and chlorofluorocarbons (CFCs), due to their prohibition under the Montreal Protocol, have suppressed an increase in total fluorine caused by increasing mixing ratios of hydrofluorocarbons (HFCs). This has reduced the impact of fluorine-containing species on global warming.

We observed ozone (O3) in the vertical region between 250 and 0.0005 hPa (~ 12–96 km) using the Superconducting Submillimeter-Wave Limb-Emission Sounder (SMILES) on the Japanese Experiment Module (JEM) of the International Space Station (ISS) between 12 October 2009 and 21 April 2010. The new 4 K superconducting heterodyne receiver technology of SMILES allowed us to obtain a one order of magnitude better signal-to-noise ratio for the O3 line observation compared to past spaceborne microwave instruments. The non-sun-synchronous orbit of the ISS allowed us to observe O3 at various local times. We assessed the quality of the vertical profiles of O3 in the 100–0.001 hPa (~ 16–90 km) region for the SMILES NICT Level 2 product version 2.1.5. The evaluation is based on four components: error analysis; internal comparisons of observations targeting three different instrumental setups for the same O3 625.371 GHz transition; internal comparisons of two different retrieval algorithms; and external comparisons for various local times with ozonesonde, satellite and balloon observations (ENVISAT/MIPAS, SCISAT/ACE-FTS, Odin/OSIRIS, Odin/SMR, Aura/MLS, TELIS). SMILES O3 data have an estimated absolute accuracy of better than 0.3 ppmv (3%) with a vertical resolution of 3–4 km over the 60 to 8 hPa range. The random error for a single measurement is better than the estimated systematic error, being less than 1, 2, and 7%, in the 40–1, 80–0.1, and 100–0.004 hPa pressure regions, respectively. SMILES O3 abundance was 10–20% lower than all other satellite measurements at 8–0.1 hPa due to an error arising from uncertainties of the tangent point information and the gain calibration for the intensity of the spectrum. SMILES O3 from observation frequency Band-B had better accuracy than that from Band-A. A two month period is required to accumulate measurements covering 24 h in local time of O3 profile. However such a dataset can also contain variation due to dynamical, seasonal, and latitudinal effects.

The European MyOcean project (http://www.myocean.eu.org) provides observations of the ocean dynamic topography from altimeter measurements. Three specific indicators have been developed, based on altimeter data only, in order to monitor the ocean state. The first ocean indicator observes the positive and negative phases of the ENSO events in the tropical Pacific, the El Niño/La Niña events, since 1992. The second ocean indicator tracks the contracted or extended state of the Kuroshio Extension. The last ocean indicator is dedicated to the Ionian Basin in the Mediterranean Sea and permits separation of "zonal-cyclonic" state (1998–2005 and since 2011 up to now) from the "anticyclonic" state (1993–1996) usually discussed in the literature. In addition, it allows identifying a third state in which both the anticyclonic circulation around the northern part of the basin and the strong zonal Mid-Ionian Jet co-exist (2008–2010).

The French program Coriolis, as part of the French operational oceanographic system, produces the COriolis dataset for Re-Analysis (CORA) on a yearly basis. This dataset contains in-situ temperature and salinity profiles from different data types. The latest release CORA3 covers the period 1990 to 2010. Several tests have been developed to ensure a homogeneous quality control of the dataset and to meet the requirements of the physical ocean reanalysis activities (assimilation and validation). Improved tests include some simple tests based on comparison with climatology and a model background check based on a global ocean reanalysis. Visual quality control is performed on all suspicious temperature and salinity profiles identified by the tests, and quality flags are modified in the dataset if necessary. In addition, improved diagnostic tools have been developed – including global ocean indicators – which give information on the quality of the CORA3 dataset and its potential applications. CORA3 is available on request through the MyOcean Service Desk (http://www.myocean.eu/).

This computational research study attempts to explain the process that leads to volume expansion during insertion of lithium ions into a silicon nanowire. During lithiation, electrons flow through the nanowire in the opposing direction of lithium ions insertion. This causes an applied electromagnetic field which is described as being a quantum mechanical version of photon density wave theory. A series of events are calculated as the individual electrons and photons travels through the lithiated silicon nanowire. The hypothesis that will be presented employs the Maxwell stress tensor to calculate the refractive indices in three orthogonal directions during lithiation. The quantum harmonic oscillator and the electromagnetic intensity will be utilized in this presentation to calculate the energy of electrons and optical amplification of the electromagnetic field respectively. The main focus of this research study will use electron scattering theory, spontaneous and stimulated emission theory to model the breaking of cohesion bonds between silicon atoms that ultimately leads to excessive volume expansion that is witnessed during the lithiation process in Si nanowires.

The Optical Spectrograph and Infra-Red Imager System (OSIRIS) and the Atmospheric Chemistry Experiment (ACE) have been taking measurements from space since 2001 and 2003, respectively. This paper presents intercomparisons between ozone and NO2 measured by the ACE and OSIRIS satellite instruments and by ground-based instruments at the Polar Environment Atmospheric Research Laboratory (PEARL), which is located at Eureka, Canada (80° N, 86° W) and is operated by the Canadian Network for the Detection of Atmospheric Change (CANDAC). The ground-based instruments included in this study are four zenith-sky differential optical absorption spectroscopy (DOAS) instruments, one Bruker Fourier transform infrared spectrometer (FTIR) and four Brewer spectrophotometers. Ozone total columns measured by the DOAS instruments were retrieved using new Network for the Detection of Atmospheric Composition Change (NDACC) guidelines and agree to within 3.2%. The DOAS ozone columns agree with the Brewer spectrophotometers with mean relative differences that are smaller than 1.5%. This suggests that for these instruments the new NDACC data guidelines were successful in producing a homogenous and accurate ozone dataset at 80° N. Satellite 14–52 km ozone and 17–40 km NO2 partial columns within 500 km of PEARL were calculated for ACE-FTS Version 2.2 (v2.2) plus updates, ACE-FTS v3.0, ACE-MAESTRO (Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) v1.2 and OSIRIS SaskMART v5.0x ozone and Optimal Estimation v3.0 NO2 data products. The new ACE-FTS v3.0 and the validated ACE-FTS v2.2 partial columns are nearly identical, with mean relative differences of 0.0 ± 0.2% and −0.2 ± 0.1% for v2.2 minus v3.0 ozone and NO2, respectively. Ozone columns were constructed from 14–52 km satellite and 0–14 km ozonesonde partial columns and compared with the ground-based total column measurements. The satellite-plus-sonde measurements agree with the ground-based ozone total columns with mean relative differences of 0.1–7.3%. For NO2, partial columns from 17 km upward were scaled to noon using a photochemical model. Mean relative differences between OSIRIS, ACE-FTS and ground-based NO2 measurements do not exceed 20%. ACE-MAESTRO measures more NO2 than the other instruments, with mean relative differences of 25–52%. Seasonal variation in the differences between NO2 partial columns is observed, suggesting that there are systematic errors in the measurements and/or the photochemical model corrections. For ozone spring-time measurements, additional coincidence criteria based on stratospheric temperature and the location of the polar vortex were found to improve agreement between some of the instruments. For ACE-FTS v2.2 minus Bruker FTIR, the 2007–2009 spring-time mean relative difference improved from −5.0 ± 0.4% to −3.1 ± 0.8% with the dynamical selection criteria. This was the largest improvement, likely because both instruments measure direct sunlight and therefore have well-characterized lines-of-sight compared with scattered sunlight measurements. For NO2, the addition of a ±1° latitude coincidence criterion improved spring-time intercomparison results, likely due to the sharp latitudinal gradient of NO2 during polar sunrise. The differences between satellite and ground-based measurements do not show any obvious trends over the missions, indicating that both the ACE and OSIRIS instruments continue to perform well.