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1.
ACS EST Air ; 1(3): 175-187, 2024 Mar 08.
Article in English | MEDLINE | ID: mdl-38482267

ABSTRACT

The oxidative potential (OP) of outdoor PM2.5 in wintertime Fairbanks, Alaska, is investigated and compared to those in wintertime Atlanta and Los Angeles. Approximately 40 filter samples collected in January-February 2022 at a Fairbanks residential site were analyzed for OP utilizing dithiothreitol-depletion (OPDTT) and hydroxyl-generation (OPOH) assays. The study-average PM2.5 mass concentration was 12.8 µg/m3, with a 1 h average maximum of 89.0 µg/m3. Regression analysis, correlations with source tracers, and contrast between cold and warmer events indicated that OPDTT was mainly sensitive to copper, elemental carbon, and organic aerosol from residential wood burning, and OPOH to iron and organic aerosol from vehicles. Despite low photochemically-driven oxidation rates, the water-soluble fraction of OPDTT was unusually high at 77%, mainly from wood burning emissions. In contrast to other locations, the Fairbanks average PM2.5 mass concentration was higher than Atlanta and Los Angeles, whereas OPDTT in Fairbanks and Atlanta were similar, and Los Angeles had the highest OPDTT and OPOH. Site differences were observed in OP when normalized by both the volume of air sampled and the particle mass concentration, corresponding to exposure and the intrinsic health-related properties of PM2.5, respectively. The sensitivity of OP assays to specific aerosol components and sources can provide insights beyond the PM2.5 mass concentration when assessing air quality.

2.
ACS EST Air ; 1(3): 188-199, 2024 Mar 08.
Article in English | MEDLINE | ID: mdl-38482268

ABSTRACT

The indoor air quality of a residential home during winter in Fairbanks, Alaska, was investigated and contrasted with outdoor levels. Twenty-four-hour average indoor and outdoor filter samples were collected from January 17 to February 25, 2022, in a residential area with high outdoor PM2.5 concentrations. The oxidative potential of PM2.5 was determined using the dithiothreitol-depletion assay (OPDTT). For the unoccupied house, the background indoor-to-outdoor (I/O) ratio of mass-normalized OP (OPmDTT), a measure of the intrinsic health-relevant properties of the aerosol, was less than 1 (0.53 ± 0.37), implying a loss of aerosol toxicity as air was transported indoors. This may result from transport and volatility losses driven by the large gradients in temperature (average outdoor temperature of -19°C/average indoor temperature of 21 °C) or relative humidity (average outdoor RH of 78%/average indoor RH of 11%), or both. Various indoor activities, including pellet stove use, simple cooking experiments, incense burning, and mixtures of these activities, were conducted. The experiments produced PM2.5 with a highly variable OPmDTT. PM2.5 from cooking emissions had the lowest OP values, while pellet stove PM2.5 had the highest. Correlations between volume-normalized OPDTT (OPvDTT), relevant to exposure, and indoor PM2.5 mass concentration during experiments were much lower compared to those in outdoor environments. This suggests that mass concentration alone can be a poor indicator of possible adverse effects of various indoor emissions. These findings highlight the importance of considering both the quantity of particles and sources (chemical composition), as health metrics for indoor air quality.

3.
ACS EST Air ; 1(3): 200-222, 2024 Mar 08.
Article in English | MEDLINE | ID: mdl-38482269

ABSTRACT

The Alaskan Layered Pollution And Chemical Analysis (ALPACA) field experiment was a collaborative study designed to improve understanding of pollution sources and chemical processes during winter (cold climate and low-photochemical activity), to investigate indoor pollution, and to study dispersion of pollution as affected by frequent temperature inversions. A number of the research goals were motivated by questions raised by residents of Fairbanks, Alaska, where the study was held. This paper describes the measurement strategies and the conditions encountered during the January and February 2022 field experiment, and reports early examples of how the measurements addressed research goals, particularly those of interest to the residents. Outdoor air measurements showed high concentrations of particulate matter and pollutant gases including volatile organic carbon species. During pollution events, low winds and extremely stable atmospheric conditions trapped pollution below 73 m, an extremely shallow vertical scale. Tethered-balloon-based measurements intercepted plumes aloft, which were associated with power plant point sources through transport modeling. Because cold climate residents spend much of their time indoors, the study included an indoor air quality component, where measurements were made inside and outside a house to study infiltration and indoor sources. In the absence of indoor activities such as cooking and/or heating with a pellet stove, indoor particulate matter concentrations were lower than outdoors; however, cooking and pellet stove burns often caused higher indoor particulate matter concentrations than outdoors. The mass-normalized particulate matter oxidative potential, a health-relevant property measured here by the reactivity with dithiothreiol, of indoor particles varied by source, with cooking particles having less oxidative potential per mass than pellet stove particles.

4.
Cureus ; 15(1): e34263, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36855492

ABSTRACT

Introduction Cardiac catheterization is an essential component of patient care in Acute Coronary Syndrome (ACS). Fecal occult blood testing (FOBT) has been used in the inpatient setting to evaluate the risk of bleeding with dual anti-platelet therapy prior to cardiac catheterization although no guidelines exist for this indication and FOBT testing in the inpatient setting is not recommended for evaluation of GI blood loss. We sought to assess the outcomes of patients with fecal occult positive stool prior to cardiac catheterization compared to those that did not undergo FOBT during admission for non-ST-elevation myocardial infarction (NSTEMI). Methods We identified patients between 18 and 90 years old with admission for NSTEMI in the Trinetx Research Network from January 1, 2019 to December 31, 2020. Patients were then divided into those who had an FOBT prior to cardiac catheterization and those that did not have an FOBT. We compared all-cause mortality, bleeding, troponin levels, and length of stay between propensity-matched (PSM) pairs of patients. Results We identified 46,349 that met inclusion criteria, of which 1,728 had an FOBT (3.7%) and 44,621 (96.3%) had no FOBT prior to cardiac catheterization. Patients in the FOBT group were older and had a higher prevalence of hypertension, coronary artery disease, heart failure, diabetes, chronic obstructive pulmonary disease, and higher BMI. Two well-matched groups of n=1,728/1,728 were used for comparing outcomes. The FOBT group had similar 30-day mortality (4.45% vs 4.01, P=0.56) as well as similar bleeding events (0.98% vs 0.69%, P=0.35). Troponin levels in the FOBT group were on average lower (0.41 vs 0.95, P=0.04). The FOBT groups also had a similar average length of stay of (14.1 days vs 14.2 days, P=0.42). 233 patients who received FOBT underwent endoscopic evaluation with either upper endoscopy or colonoscopy (13.5%), and there was no significant difference in 30-day mortality (6.86% vs 4.7%, P=0.321). Among patients who underwent endoscopy, 72 had some form of endoscopic intervention (30.9%). There was no difference in 30-day mortality between patients undergoing endoscopy with intervention and without intervention (14.49%/14.49%) P=1.00. Readmission was similar between patients undergoing endoscopy with and without intervention. Conclusions In a large multi-center national database, we observed similar outcomes in patients who were admitted with NSTEMI and had FOBT and those not receiving FOBT in terms of all-cause mortality and bleeding events. In patients with positive FOBT, endoscopy with and without intervention we observed no significant difference in 30-day mortality. We conclude that there is no compelling evidence for FOBT testing in patients with NSTEMI.

5.
Environ Sci Technol ; 56(12): 7657-7667, 2022 06 21.
Article in English | MEDLINE | ID: mdl-35544773

ABSTRACT

Fairbanks, Alaska, is a subarctic city with fine particle (PM2.5) concentrations that exceed air quality regulations in winter due to weak dispersion caused by strong atmospheric inversions, local emissions, and the unique chemistry occurring under the cold and dark conditions. Here, we report on observations from the winters of 2020 and 2021, motivated by our pilot study that showed exceptionally high concentrations of fine particle hydroxymethanesulfonate (HMS) or related sulfur(IV) species (e.g., sulfite and bisulfite). We deployed online particle-into-liquid sampler-ion chromatography (PILS-IC) in conjunction with a suite of instruments to determine HMS precursors (HCHO, SO2) and aerosol composition in general, with the goal to characterize the sources and sinks of HMS in wintertime Fairbanks. PM2.5 HMS comprised a significant fraction of PM2.5 sulfur (26-41%) and overall PM2.5 mass concentration of 2.8-6.8% during pollution episodes, substantially higher than what has been observed in other regions, likely due to the exceptionally low temperatures. HMS peaked in January, with lower concentrations in December and February, resulting from changes in precursors and meteorological conditions. Strong correlations with inorganic sulfate and organic mass during pollution events suggest that HMS is linked to processes responsible for poor air quality episodes. These findings demonstrate unique aspects of air pollution formation in cold and humid atmospheres.


Subject(s)
Air Pollutants , Air Pollution , Aerosols/chemistry , Air Pollutants/analysis , Air Pollution/analysis , Alaska , Environmental Monitoring/methods , Particulate Matter/analysis , Pilot Projects , Seasons , Sulfur
6.
J Agric Food Chem ; 69(27): 7687-7697, 2021 Jul 14.
Article in English | MEDLINE | ID: mdl-34180657

ABSTRACT

Condensed tannin extraction and stable color formation are two of the cornerstones of red wine production. Without condensed tannin, red wine would lack the tactile feeling of astringency, and without the formation of modified pigments, it would lack color stability for long-term aging. To understand how malvidin-3,5-diglucoside interacts with condensed tannin under nonoxidative conditions, an experiment was designed conducting model-wine skin extractions of Sauvignon blanc grapes harvested at various dates of maturity. Monomeric malvidin-3,5-diglucoside was isolated from color concentrate and added during these extractions. Following a 72 h extraction, solutions were evaluated for recovery of monomeric anthocyanins, skin tannin concentration, skin tannin extractability, and impact of anthocyanins on condensed tannin size. Anthocyanins showed a significant impact on the extraction of flavan-3-ol material in the early stages of ripening that declined in the latter stages of ripening. Furthermore, anthocyanins significantly decreased the size of the condensed tannin extracted. These results suggest that anthocyanins are not only enhancing the extractability of condensed tannin but also readily incorporating into the polymeric material, leading to a decrease in the average molecular mass of the condensed tannin polymer. The extent of reaction in 72 h suggests that the rate of interflavan bond cleavage may be higher than previously reported and merits closer scrutiny.


Subject(s)
Vitis , Wine , Anthocyanins/analysis , Color , Fruit/chemistry , Molecular Weight , Tannins/analysis , Wine/analysis
7.
N Engl J Med ; 384(21): 1981-1990, 2021 05 27.
Article in English | MEDLINE | ID: mdl-33999548

ABSTRACT

BACKGROUND: The appropriate dose of aspirin to lower the risk of death, myocardial infarction, and stroke and to minimize major bleeding in patients with established atherosclerotic cardiovascular disease is a subject of controversy. METHODS: Using an open-label, pragmatic design, we randomly assigned patients with established atherosclerotic cardiovascular disease to a strategy of 81 mg or 325 mg of aspirin per day. The primary effectiveness outcome was a composite of death from any cause, hospitalization for myocardial infarction, or hospitalization for stroke, assessed in a time-to-event analysis. The primary safety outcome was hospitalization for major bleeding, also assessed in a time-to-event analysis. RESULTS: A total of 15,076 patients were followed for a median of 26.2 months (interquartile range [IQR], 19.0 to 34.9). Before randomization, 13,537 (96.0% of those with available information on previous aspirin use) were already taking aspirin, and 85.3% of these patients were previously taking 81 mg of daily aspirin. Death, hospitalization for myocardial infarction, or hospitalization for stroke occurred in 590 patients (estimated percentage, 7.28%) in the 81-mg group and 569 patients (estimated percentage, 7.51%) in the 325-mg group (hazard ratio, 1.02; 95% confidence interval [CI], 0.91 to 1.14). Hospitalization for major bleeding occurred in 53 patients (estimated percentage, 0.63%) in the 81-mg group and 44 patients (estimated percentage, 0.60%) in the 325-mg group (hazard ratio, 1.18; 95% CI, 0.79 to 1.77). Patients assigned to 325 mg had a higher incidence of dose switching than those assigned to 81 mg (41.6% vs. 7.1%) and fewer median days of exposure to the assigned dose (434 days [IQR, 139 to 737] vs. 650 days [IQR, 415 to 922]). CONCLUSIONS: In this pragmatic trial involving patients with established cardiovascular disease, there was substantial dose switching to 81 mg of daily aspirin and no significant differences in cardiovascular events or major bleeding between patients assigned to 81 mg and those assigned to 325 mg of aspirin daily. (Funded by the Patient-Centered Outcomes Research Institute; ADAPTABLE ClinicalTrials.gov number, NCT02697916.).


Subject(s)
Aspirin/administration & dosage , Cardiovascular Diseases/drug therapy , Platelet Aggregation Inhibitors/administration & dosage , Aged , Aspirin/adverse effects , Atherosclerosis/drug therapy , Cardiovascular Diseases/mortality , Cardiovascular Diseases/prevention & control , Female , Hemorrhage/chemically induced , Hospitalization , Humans , Male , Medication Adherence/statistics & numerical data , Middle Aged , Myocardial Infarction/epidemiology , Myocardial Infarction/prevention & control , Platelet Aggregation Inhibitors/adverse effects , Secondary Prevention , Stroke/epidemiology , Stroke/prevention & control
8.
JCO Clin Cancer Inform ; 4: 724-735, 2020 08.
Article in English | MEDLINE | ID: mdl-32795185

ABSTRACT

PURPOSE: Examine the ability of PCORnet data resources to investigate molecular-guided cancer treatment. PATIENTS AND METHODS: Patients (N = 86,154) had single primary solid tumors (diagnosed 2013-2017) from hospital oncology registries linked to the PCORnet Common Data Model (CDM) at 11 medical institutions. Molecular and anatomic test procedures and oral and infused therapies were identified with Current Procedural Terminology (CPT) and Healthcare Common Procedure Coding System (HCPCS) codes, RxNorm Concept Unique Identifier, and National Drug Codes from CDM tables. Chart review (2 institutions, n = 213) for advanced colorectal cancer and Medicare claims linkages (7 institutions, n = 1,731) for breast cancer explored options for increasing electronic data capture. RESULTS: Molecular testing prevalence detected via analyte-specific molecular CPT/HCPCS codes was 5.5% (n = 4,784); for the nonspecific anatomic pathology codes, for which only some testing is performed to guide therapy selection, it was an additional 44.8% (n = 38,610). Molecular-guided therapy prevalence was 5% (n = 4,289). Testing and treatment were most common with stage IV disease and varied across cancer types and study institutions (testing, 0%-10.4%; treatment, 0.8%-8.4%). Therapy-concordant test results were found in charts for all 36 treated patients with colorectal cancer at the 2 institutions, 3 (8.3%) of whom received treatment outside the institution. Breast cancer Medicare claims linkage increased rates of identified testing from 62.7%-98.9% and treatment from 3.9%-8.2%. CONCLUSION: Although a minority of patients received molecular-guided therapies, the majority had testing that could guide cancer treatment. Claims data extended electronic data capture for therapies and test orders but often was uninformative for types of test ordered. Test results continue to require text data curation from narrative pathology reports.


Subject(s)
Colorectal Neoplasms , Medicare , Aged , Current Procedural Terminology , Humans , Registries , United States/epidemiology
9.
Int J Med Inform ; 126: 19-25, 2019 06.
Article in English | MEDLINE | ID: mdl-31029260

ABSTRACT

OBJECTIVE: Clinical problems in the Electronic Health Record that are encoded in SNOMED CT can be translated into ICD-10-CM codes through the NLM's SNOMED CT to ICD-10-CM map (NLM Map). This study evaluates the potential benefits of using the map-generated codes to assist manual ICD-10-CM coding. METHODS: De-identified clinic notes taken by the physician during an outpatient encounter were made available on a secure web server and randomly assigned for coding by professional coders with usual coding or map-assisted coding. Map-assisted coding made use of the problem list maintained by the physician and the NLM Map to suggest candidate ICD-10-CM codes to the coder. A gold standard set of codes for each note was established by the coders using a Delphi consensus process. Outcomes included coding time, coding reliability as measured by the Jaccard coefficients between codes from two coders with the same method of coding, and coding accuracy as measured by recall, precision and F-score according to the gold standard. RESULTS: With map-assisted coding, the average coding time per note reduced by 1.5 min (p = 0.006). There was a small increase in coding reliability and accuracy (not statistical significant). The benefits were more pronounced in the more experienced than less experienced coders. Detailed analysis of cases in which the correct ICD-10-CM codes were not found by the NLM Map showed that most failures were related to omission in the problem list and suboptimal mapping of the problem list terms to SNOMED CT. Only 12% of the failures was caused by errors in the NLM Map. CONCLUSION: Map-assisted coding reduces coding time and can potentially improve coding reliability and accuracy, especially for more experienced coders. More effort is needed to improve the accuracy of the map-suggested ICD-10-CM codes.


Subject(s)
International Classification of Diseases , Systematized Nomenclature of Medicine , Ambulatory Care Facilities , Electronic Health Records , Humans , Outpatients , Physicians , Reproducibility of Results
10.
J Mol Diagn ; 21(3): 408-417, 2019 05.
Article in English | MEDLINE | ID: mdl-30797065

ABSTRACT

Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. Genetic sequence test results are typically communicated by the molecular laboratory and stored in the EHR as textual documents. Although text documents are useful for human readability and initial use, they are not conducive for data retrieval and reuse. As a result, clinicians often struggle to find historical gene sequence results on a series of oncology patients within the EHR that might influence the care of the current patient. Second, identification of patients with specific mutation results in the EHR who are now eligible for new and/or changing therapy is not easily accomplished. Third, the molecular laboratory is challenged to monitor its sequencing processes for nonrandom process variation and other quality metrics. A novel approach to address each of these issues is presented and demonstrated. The authors use standard Health Level 7 laboratory result message formats in conjunction with international standards, Systematized Nomenclature of Medicine Clinical Terms and Human Genome Variant Society nomenclature, to represent, communicate, and store discrete gene sequence data within the EHR in a scalable fashion. This information management plan enables the support of the clinician at the point of care, enhances population management, and facilitates audits for maintaining laboratory quality.


Subject(s)
Electronic Health Records , Pathology, Molecular/standards , Sequence Analysis, DNA/standards , Base Sequence , High-Throughput Nucleotide Sequencing , Humans , Reference Standards , Terminology as Topic
11.
Atmos Chem Phys ; 19(1): 205-218, 2019 Jan 07.
Article in English | MEDLINE | ID: mdl-33414816

ABSTRACT

We conceptualize aerosol radiative transfer processes arising from the hypothetical coupling of a global aerosol transport model and a global numerical weather prediction model by applying the US Naval Research Laboratory Navy Aerosol Analysis and Prediction System (NAAPS) and the Navy Global Environmental Model (NAVGEM) meteorological and surface reflectance fields. A unique experimental design during the 2013 NASA Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) field mission allowed for collocated airborne sampling by the high spectral resolution Lidar (HSRL), the Airborne Multi-angle SpectroPolarimetric Imager (AirMSPI), up/down shortwave (SW) and infrared (IR) broadband radiometers, as well as NASA A-Train support from the Moderate Resolution Imaging Spectroradiometer (MODIS), to attempt direct aerosol forcing closure. The results demonstrate the sensitivity of modeled fields to aerosol radiative fluxes and heating rates, specifically in the SW, as induced in this event from transported smoke and regional urban aerosols. Limitations are identified with respect to aerosol attribution, vertical distribution, and the choice of optical and surface polarimetric properties, which are discussed within the context of their influence on numerical weather prediction output that is particularly important as the community propels forward towards inline aerosol modeling within global forecast systems.

13.
Atmos Meas Tech ; 11(1): 499-514, 2018 Jan.
Article in English | MEDLINE | ID: mdl-33868502

ABSTRACT

Due to instrument sensitivities and algorithm detection limits, level 2 (L2) Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) 532nm aerosol extinction profile retrievals are often populated with retrieval fill values (RFVs), which indicate the absence of detectable levels of aerosol within the profile. In this study, using 4 years (2007-2008 and 2010-2011) of CALIOP version 3 L2 aerosol data, the occurrence frequency of daytime CALIOP profiles containing all RFVs (all-RFV profiles) is studied. In the CALIOP data products, the aerosol optical thickness (AOT) of any all-RFV profile is reported as being zero, which may introduce a bias in CALIOP-based AOT climatologies. For this study, we derive revised estimates of AOT for all-RFV profiles using collocated Moderate Resolution Imaging Spectroradiometer (MODIS) Dark Target (DT) and, where available, AErosol RObotic NEtwork (AERONET) data. Globally, all-RFV profiles comprise roughly 71% of all daytime CALIOP L2 aerosol profiles (i.e., including completely attenuated profiles), accounting for nearly half (45 %) of all daytime cloud-free L2 aerosol profiles. The mean collocated MODIS DT (AERONET) 550 nm AOT is found to be near 0.06 (0.08) for CALIOP all-RFV profiles. We further estimate a global mean aerosol extinction profile, a so-called "noise floor", for CALIOP all-RFV profiles. The global mean CALIOP AOT is then recomputed by replacing RFV values with the derived noise-floor values for both all-RFV and non-all-RFV profiles. This process yields an improvement in the agreement of CALIOP and MODIS over-ocean AOT.

14.
Article in English | MEDLINE | ID: mdl-31360778

ABSTRACT

Intense heating by wildfires can generate deep, smoke-infused thunderstorms, known as pyrocumulonimbus (pyroCb), which can release a large quantity of smoke particles above jet aircraft cruising altitudes. Injections of pyroCb smoke into the lower stratosphere have gained increasing attention over the past 15 years due to the rapid proliferation of satellite remote sensing tools. Impacts from volcanic eruptions and other troposphere-to-stratosphere exchange processes on stratospheric radiative and chemical equilibrium are well recognized and monitored. However, the role of pyroCb smoke in the climate system has yet to be acknowledged. Here, we show that the mass of smoke aerosol particles injected into the lower stratosphere from five near-simultaneous intense pyroCbs occurring in western North America on 12 August 2017 was comparable to that of a moderate volcanic eruption, and an order of magnitude larger than previous benchmarks for extreme pyroCb activity. The resulting stratospheric plume encircled the Northern Hemisphere over several months. By characterizing this event, we conclude that pyroCb activity, considered as either large singular events, or a full fire season inventory, significantly perturb the lower stratosphere in a manner comparable with infrequent volcanic intrusions.

15.
J Am Med Inform Assoc ; 25(3): 259-266, 2018 Mar 01.
Article in English | MEDLINE | ID: mdl-29024958

ABSTRACT

BACKGROUND: The College of American Pathologists (CAP) introduced the first cancer synoptic reporting protocols in 1998. However, the objective of a fully computable and machine-readable cancer synoptic report remains elusive due to insufficient definitional content in Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) and Logical Observation Identifiers Names and Codes (LOINC). To address this terminology gap, investigators at the University of Nebraska Medical Center (UNMC) are developing, authoring, and testing a SNOMED CT observable ontology to represent the data elements identified by the synoptic worksheets of CAP. METHODS: Investigators along with collaborators from the US National Library of Medicine, CAP, the International Health Terminology Standards Development Organization, and the UK Health and Social Care Information Centre analyzed and assessed required data elements for colorectal cancer and invasive breast cancer synoptic reporting. SNOMED CT concept expressions were developed at UNMC in the Nebraska Lexicon© SNOMED CT namespace. LOINC codes for each SNOMED CT expression were issued by the Regenstrief Institute. SNOMED CT concepts represented observation answer value sets. RESULTS: UNMC investigators created a total of 194 SNOMED CT observable entity concept definitions to represent required data elements for CAP colorectal and breast cancer synoptic worksheets, including biomarkers. Concepts were bound to colorectal and invasive breast cancer reports in the UNMC pathology system and successfully used to populate a UNMC biobank. DISCUSSION: The absence of a robust observables ontology represents a barrier to data capture and reuse in clinical areas founded upon observational information. Terminology developed in this project establishes the model to characterize pathology data for information exchange, public health, and research analytics.

16.
AMIA Annu Symp Proc ; 2016: 352-360, 2016.
Article in English | MEDLINE | ID: mdl-28269830

ABSTRACT

Molecular genetics laboratory reports are multiplying and increasingly of clinical importance in diagnosis and treatment of cancer, infectious disease and managing of public health. Little of this data is structured or maintained in the EHR in format useful for decision support or research. Structured, computable reporting is limited by non-availability of a domain ontology for these data. The IHTSDO and Regenstrief Institute(RI) have been collaborating since 2008 to develop a unified concept model and ontology of observable entities - concepts which represent the results of laboratory and clinical observations. In this paper we report the progress we have made to apply that unified concept model to the structured recording of observations in clinical molecular genetic pathology including immunohistochemistry and sequence variant findings. The primary use case for deployment is the structured and coded reporting of Cancer checklist


Subject(s)
Gene Ontology , Molecular Biology , Systematized Nomenclature of Medicine , Biomarkers, Tumor , Humans , Logical Observation Identifiers Names and Codes , Models, Theoretical , Molecular Biology/classification
17.
J Atmos Ocean Technol ; Volume 33(Iss 10): 2113-2134, 2016 Oct.
Article in English | MEDLINE | ID: mdl-32440037

ABSTRACT

The National Aeronautics and Space Administration Micropulse Lidar Network Version 3 cloud detection algorithm is described and its differences relative to the previous version highlighted. Clouds are identified from normalized Level 1 signal profiles using two complementary methods. The first considers signal derivatives vertically for resolving low-level clouds. The second, which resolves high-level clouds like cirrus, is based on signal uncertainties given the relatively low signal-to-noise ratio exhibited in the upper troposphere by eye-safe network instruments, especially during daytime. Furthermore, a multi-temporal averaging scheme is used to improve cloud detection under conditions of weak signal-to-noise. Diurnal and seasonal cycles of cloud occurrence frequency based on one year of measurements at the Goddard Space Flight Center (Greenbelt, MD) site are compared for the new and previous versions. The largest differences, and perceived improvement, in detection occurs for high clouds (above 5-km, mean sea level) which increase in occurrence by nearly 6%. There is also an increase in the detection of multi-layered cloud profiles from 9% to 20%. Macrophysical properties and estimates of cloud optical depth are presented for a transparent cirrus dataset. However, the limit to which molecular signal can be reliably retrieved above cirrus clouds occurs between cloud optical depths of 0.5 and 0.8.

18.
Aerosol Air Qual Res ; 16(11): 2818-2830, 2016 Nov 01.
Article in English | MEDLINE | ID: mdl-32747859

ABSTRACT

As part of the Seven Southeast Asian Studies (7SEAS) program, an Aerosol Robotic Network (AERONET) sun photometer and a Micro-Pulse Lidar Network (MPLNET) instrument have been deployed at Singapore to study the regional aerosol environment of the Maritime Continent (MC). In addition, the Navy Aerosol Analysis and Prediction System (NAAPS) is used to model aerosol transport over the region. From 24 September 2009 to 31 March 2011, the relationships between ground-, satellite- and model-based aerosol optical depth (AOD) and particulate matter with aerodynamic equivalent diameters less than 2.5 µm (PM2.5) for air quality applications are investigated. When MPLNET-derived aerosol scale heights are applied to normalize AOD for comparison with surface PM2.5 data, the empirical relationships are shown to improve with an increased 11 %, 10 % and 5 % in explained variances, for AERONET, MODIS and NAAPS respectively. The ratios of root mean square errors to standard deviations for the relationships also show corresponding improvements of 8 %, 6 % and 2 %. Aerosol scale heights are observed to be bimodal with a mode below and another above the strongly-capped/deep near-surface layer (SCD; 0 - 1.35 km). Aerosol extinctions within SCD are well-correlated with surface PM2.5 concentrations, possibly due to strong vertical mixing in the region.

19.
J Appl Meteorol Climatol ; 55(8): 1667-1679, 2016 Aug.
Article in English | MEDLINE | ID: mdl-32818026

ABSTRACT

One-year of continuous ground-based lidar observations (2012) are analyzed for single-layer cirrus clouds at the NASA Micro Pulse Lidar Network site at the Goddard Space Flight Center to investigate top-of-atmosphere (TOA) annual net daytime radiative forcing properties. A slight positive net daytime forcing is estimated (i.e., warming) : 0.07 - 0.67 W/m2 in relative terms, which reduces to 0.03 - 0.27 W/m2 in absolute terms after normalizing to unity based on approximated 40% midlatitude occurrence frequency rate estimated from satellite. Results are based on bookend solutions for lidar extinction-to-backscatter (20 and 30 sr) and corresponding retrievals for 532 nm cloud extinction coefficient. Uncertainties due to cloud undersampling, attenuation effects, sample selection and lidar multiple scattering are described. A net daytime cooling effect is found from the very thinnest clouds (cloud optical depth ≤ 0.01) that is attributed to relatively high solar zenith angles. A relationship between positive/negative daytime cloud forcing is demonstrated as a function of solar zenith angle and cloud top temperature. These properties, combined with the influence of varying surface albedos, are used to conceptualize how daytime cloud forcing likely varies with latitude and season, with cirrus clouds exerting less positive forcing and potentially net TOA cooling approaching the summer poles (non-ice and snow covered) versus greater warming at the equator. The existence of such a gradient would lead cirrus to induce varying daytime TOA forcing annually and seasonally, making it a far greater challenge than presently believe to constrain daytime and diurnal cirrus contributions to global radiation budgets.

20.
Ann Surg ; 262(3): 495-501; discussion 500-1, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26258318

ABSTRACT

OBJECTIVE: To compare with antibiotics with methicillin-resistant microbial coverage in a prospective fashion. BACKGROUND: Current antibiotic prophylaxis for vascular procedures includes a first generation cephalosporin. No changes in recommendations have occurred despite changes in reports of incidence of MRSA related surgical site infections. Does supplemental anti-MRSA prophylactic coverage provide a significant reduction in Gram-positive or MRSA infections? METHODS: Single center prospective double blinded randomized study of patients undergoing lower extremity vascular procedures from 2011 to 2014. One hundred seventy-eight (178) patients were evaluated at 90 days for surgical site infection. Infections were categorized as early infections less than 30 days of the index procedure and late after 90 days. RESULTS: Early vascular surgical site infection occurred in 7(8.24%) of patients in the Vancomycin arm, and 11 (11.83%) in the Daptomycin arm (P = 0.43). Gram-positive related infections and MRSA infections occurred in 1(1.18%)/0(0%) of Vancomycin patients and 9 (9.68%)/1 (1.08%) of Daptomycin patients, respectively (P < 0.02 and P = 1.00). Readmissions related to surgical site infections occurred in 4(4.71%) in the Vancomycin group and 11 (11.8%) in the Daptomycin group (P = 0.11). Patients undergoing operative exploration occurred in 5 (5.88%) in the Vancomycin group and 10 (10.75%) of the Daptomycin group (P = 0.17). Late infections were reported in 3 patients, 2 of which were in the combined Daptomycin group. Median hospital charges related to readmissions due to a surgical site infection was $50,823 in the combination Vancomycin arm and $110,920 in the combination Daptomycin group; however, no statistical significance was appreciated (P = 0.11). CONCLUSIONS: Vancomycin supplemental prophylaxis seems to reduce the incidence of Gram-positive infection compared with adding supplemental Daptomycin prophylaxis. The Incidence of MRSA-related surgical site infections is low with the addition of either anti-MRSA agents compared with historical incidence of MRSA-related infection.


Subject(s)
Antibiotic Prophylaxis/methods , Methicillin-Resistant Staphylococcus aureus/drug effects , Peripheral Vascular Diseases/drug therapy , Staphylococcal Infections/prevention & control , Surgical Wound Infection/prevention & control , Vascular Surgical Procedures/methods , Adult , Aged , Cefazolin/administration & dosage , Chi-Square Distribution , Daptomycin/administration & dosage , Double-Blind Method , Drug Therapy, Combination , Female , Follow-Up Studies , Humans , Lower Extremity , Male , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Middle Aged , Patient Safety , Peripheral Vascular Diseases/diagnostic imaging , Peripheral Vascular Diseases/surgery , Preoperative Care/methods , Prospective Studies , Radiography , Risk Assessment , Treatment Outcome , Vancomycin/administration & dosage , Vascular Surgical Procedures/adverse effects
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