Vertical transport and photochemistry in the terrestrial mesosphere and lower thermosphere (50–120 km)

The coupled effects of kinetics, solar cycle flux variations and vertical transport on the distribution of long-lived hydrogen-carbon-oxygen compounds in the terrestrial mesosphere and lower thermosphere are studied using a one-dimensional aeronomy model. The calculations account for the important chemical reactions and use rocket measurements of the solar flux at solar minimum and maximum. Photodissociation rates appropriate for the mesosphere are determined with a spherical shell atmosphere formalism; detailed corrections for the O_2 Schumann-Runge bands and the temperature dependence of the CO_2 cross sections are used. Then an eddy diffusion profile is derived which gives agreement with the Aladdin 74 mass spectral measurements of atomic O, O_2, CO_2, and Ar in the lower thermosphere and observations of the O_3 minimum at ∼80 km. The 115 GHz CO radio emission line computed for the CO mixing ratio profile predicted with the new eddy diffusion profile compares well with recent observations of W. J. Wilson. Differences between the calculated CO mixing ratio profile and previous theoretical and observational determinations are discussed. Our derived eddy diffusion profile has a sudden decrease at 92 km which is necessary to produce the atomic O peak at 98 km that appears in the Aladdin 74 measurements. This stagnant region apparently is a recurrent or persistent feature of the upper atmosphere since an atomic O peak around 98 km has been seen by different techniques in different seasons over several years. Slow eddy diffusion in the lower thermosphere through the homopause was also the conclusion of earlier Ar/N_2 rocket measurements studies. The analytic approach of this paper could be used in the future to monitor variations in middle atmosphere dynamics, if regularly conducted simultaneous observations of various groups of species were available

Effects of negative energy balance on liver gene and protein expression during the early postpartum period and its impacts on dairy cow fertility

End of project reportNegative energy balance (NEB) is a severe metabolic affecting high yielding dairy cows early post partum with both concurrent and latent negative effects on cow fertility as well as on milk production and cow health. The seasonal nature of Irish dairy production necessitates high cow fertility and a compact spring calving pattern in order to maximise grass utilisation. Poor dairy cow reproductive performance currently costs the Irish cattle industry in excess of €400 million annually. High milk yields have been associated with lower reproductive efficiency, and it has been suggested that this effect is probably mediated through its effects on the energy balance of the cow during lactation. The modern high genetic merit dairy cow prioritises nutrient supply towards milk production in early lactation and this demand takes precedence over the provision of optimal conditions for reproduction. In this study we used the bovine Affymetrix 23,000 gene microarray, which contains the most comprehensive set of bovine genes to be assembled and provides a means of investigating the modifying influences of energy balance on liver gene expression. Cows in severe negative energy balance (SNEB) in early lactation showed altered hepatic gene expression in metabolic processes as well as a down regulation of the insulin-like growth factor (IGF) system, where insulin like growth factor-1 (IGF-1), growth hormone receptor variant 1A (GHR1A) and insulin-like growth factor binding protein-acid labile subunit (IGFBP-ALS) were down regulated compared to the cows in the moderate negative energy balance MNEB group, consistent with a five-fold reduction in systemic concentrations of IGF1 in the SNEB group.Cows in SNEB showed elevated expression of key genes involved in the inflammatory response such as interleukin-8 (IL-8). There was a down regulation of genes involved in cellular growth in SNEB cows and moreover a negative regulator of cellular proliferation (HGFIN) was up regulated in SNEB cows, which is likely to compromise adaptation and recovery from NEB. The puma method of analysis revealed that 417 genes were differentially regulated by EB (P<0.05), of these genes 190 were up-regulated while 227 were down-regulated, with 405 genes having known biological functions. From Ingenuity Pathway Analysis (IPA), lipid catabolism was found to be the process most affected by differences in EB status

Trajectory Mapping and Applications to Data from the Upper Atmosphere Research Satellite

The problem of creating synoptic maps from asynoptically gathered trace gas data has prompted the development of a number of schemes. Most notable among these schemes are the Kalman filter, the Salby-Fourier technique, and constituent reconstruction. This paper explores a new technique called trajectory mapping. Trajectory mapping creates synoptic maps from asynoptically gathered data by advecting measurements backward or forward in time using analyzed wind fields. A significant portion of this work is devoted to an analysis of errors in synoptic trajectory maps associated with the calculation of individual parcel trajectories. In particular, we have considered (1) calculational errors; (2) uncertainties in the values and locations of constituent measurements, (3) errors incurred by neglecting diabatic effects, and (4) sensitivity to differences in wind field analyses. These studies reveal that the global fields derived from the advection of large numbers of measurements are relatively insensitive to the errors in the individual trajectories. The trajectory mapping technique has been successfully applied to a variety of problems. In this paper, the following two applications demonstrate the usefulness of the technique: an analysis of dynamical wave-breaking events and an examination of Upper Atmosphere Research Satellite data accuracy

Pneumocystis pneumonia, a COVID-19 mimic, reminds us of the importance of HIV testing in COVID-19

While clinical environments are highly focused on COVID-19, reports of missed or delayed treatment for conditions that imitate COVID-19, such as pneumonia caused by the fungus Pneumocystis jirovecii, are emerging. Given the uncertain spectrum of COVID-19 presentations and variable sensitivity of laboratory tests for SARS-CoV-2, there is a risk that, without a high index of suspicion, alternative aetiologies may be overlooked while pursuing a diagnosis of COVID-19. The British HIV Association has been calling for the inclusion of HIV testing in all patients admitted to hospital with suspected COVID-19. In this article we reflect on the importance of including HIV testing to prevent avoidable morbidity and mortality in our patients.Publisher PDFPeer reviewe

Pancreatic Cysts Identification Using Unstructured Information Management Architecture

poster abstractPancreatic cancer is one of the deadliest cancers, mostly diagnosed at late stages. Patients with pancreatic cysts are at higher risk of developing cancer and surveillance of these patients can help with early diagnosis. Much information about pancreatic cysts can be found in free text format in various medical narratives. In this retrospective study, a corpus of 1064 records from 44 patients at Indiana University Hospital from 1990 to 2012 was collected. A natural language processing system was developed and used to identify patients with pancreatic cysts. The input goes through series of tasks within the Unstructured Information Management Architecture (UIMA) framework consisting of report separation, metadata detection, sentence detection, concept annotation and writing into the database. Metadata such as medical record number (MRN), report id, report name, report date, report body were extracted from each report. Sentences were detected and concepts within each sentence were extracted using regular expression. Regular expression is a pattern of characters matching specific string of text. Our medical team assembled concepts that are used to identify pancreatic cysts in medical reports and additional keywords were added by searching through literature and Unified Medical Language System (UMLS) knowledge base. The Negex Algorithm was used to find out negation status of concepts. The 1064 reports were divided into sets of train and test sets. Two pancreatic-cyst surgeons created the gold standard data (Inter annotator agreement K=88%). The training set was analyzed to modify the regular expression. The concept identification using the NegEx algorithm resulted in precision and recall of 98.9% and 89% respectively. In order to improve the performance of negation detection, Stanford Dependency parser (SDP) was used. SDP finds out how words are related to each other in a sentence. SDP based negation algorithm improved the recall to 95.7%

An investigation of the processes controlling ozone in the upper stratosphere

Photolysis of vibrationally excited oxygen produced by ultraviolet photolysis of ozone in the upper stratosphere is incorporated into the Lawrence Livermore National Laboratory 2-D zonally averaged chemical-radiative-transport model of the troposphere and stratosphere. The importance of this potential contributor of odd oxygen to the concentration of ozone is evaluated based upon recent information on vibrational distributions of excited oxygen and upon preliminary studies of energy transfer from the excited oxygen. When the energy transfer rate constants of previous work are assumed, increases in model ozone concentrations of up to 40 percent in the upper stratosphere are found, and the ozone concentrations of the model agree with measurements, including data from the Upper Atmosphere Research Satellite. However, the increase is about 0.4 percent when the larger energy transfer rate constants suggested by more recent experimental work are applied in the model. This indicates the importance of obtaining detailed information on vibrationally excited oxygen properties to evaluation of this process for stratospheric modelling

Variations of tropical upper tropospheric clouds with sea surface temperature and implications for radiative effects

The variations of tropical upper tropospheric (UT) clouds with sea surface temperature (SST) are analyzed using effective cloud fraction from the Atmospheric Infrared Sounder (AIRS) on Aqua and ice water content (IWC) from the Microwave Limb Sounder (MLS) on Aura. The analyses are limited to UT clouds above 300 hPa. Our analyses do not suggest a negative correlation of tropical-mean UT cloud fraction with the cloud-weighted SST (CWT). Instead, both tropical-mean UT cloud fraction and IWC are found to increase with CWT, although their correlations with CWT are rather weak. The rate of increase of UT cloud fraction with CWT is comparable to that of precipitation, while the UT IWC and ice water path (IWP) increase more strongly with CWT. The radiative effect of UT clouds is investigated, and they are shown to provide a net warming at the top of the atmosphere. An increase of IWP with SST yields an increase of net warming that corresponds to a positive feedback, until the UT IWP exceeds a value about 50% greater than presently observed by MLS. Further increases of the UT IWP would favor the shortwave cooling effect, causing a negative feedback. Sensitivities of UT cloud forcing to the uncertainties in UT CFR and IWC measurements are discussed

The Evolution of the Stratopause During the 2006 Major Warming: Satellite Data and Assimilated Meteorological Analyses

Microwave Limb Sounder and Sounding of the Atmosphere with Broadband Emission Radiometry data show the polar stratopause, usually higher than and separated from that at midlatitudes, dropping from <55-60 to near 30 km, and cooling dramatically in January 2006 during a major stratospheric sudden warming (SSW). After a nearly isothermal period, a cool stratopause reforms near 75 km in early February, then drops to <55 km and warms. The stratopause is separated in longitude as well as latitude, with lowest temperatures in the transition regions between higher and lower stratopauses. Operational assimilated meteorological analyses, which are not constrained by data at stratopause altitude, do not capture a secondary temperature maximum that overlies the stratopause or the very high stratopause that reforms after the SSW; they underestimate the stratopause altitude variation during the SSW. High-quality daily satellite temperature measurements are invaluable in improving our understanding of stratopause evolution and its representation in models and assimilation systems

Seasonal variations of water vapor in the tropical lower stratosphere

Measurements of stratospheric water vapor by the Microwave Limb Sounder aboard the Upper Atmosphere Research Satellite show that in the tropical lower stratosphere, low‐frequency variations are closely related to the annual cycle in tropical tropopause temperatures. Tropical stratospheric air appears to retain information about the tropopause conditions it encountered for over a year as it rises through the stratosphere. We use a two‐dimensional Lagrangian model to relate MLS measurements to the temperature that tropical air parcels encountered when crossing the 100 hPa surface

Ralph J. Perk, the “New ethnicity”, and the making of urban ethnic republicans

Historians seeking to explain the late twentieth century rightward shift of urban ethnic whites have tended to ignore the shifting meaning and content of white ethnic identity in this transition, and the utility of these changes to conservative political discourse. This article, focusing on the ethnic strategies of the Republican mayor of Cleveland, Ralph Perk, seeks to illustrate the importance of the “New Ethnicity” of the 1970s, and its reconceptualization of white ethnicity as a series of “values”, in the making of urban ethnic Republicans. In doing so it reorients our understanding of Perk – the “Ethnic Mayor” – and places ethnicity at the heart of the conservative insurgency reshaping urban and national politics during this period