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We devised a model to interpret discordant SARS-CoV-2 test results. We estimate that, during March 2020–May 2022, a patient in the United States who received a positive rapid antigen test result followed by a negative nucleic acid test result had only a 15.4% (95% CI 0.6%–56.7%) chance of being infected.
Co-infection, especially with pathogens of dissimilar genetic makeup, may result in a more devastating impact on the host. Investigations on co-infection with neglected zoonotic pathogens in wildlife are necessary to inform appropriate prevention and control strategies to reduce disease burden in wildlife and the potential transmission of these pathogens between wildlife, livestock and humans. This study assessed co-exposure of various Kenyan wildflife species with Brucella spp, Coxiella burnetii and Rift Valley fever virus (RVFV). A total of 363 sera from 16 different wildlife species, most of them (92.6%) herbivores, were analysed by Enzyme-linked immunosorbent assay (ELISA) for IgG antibodies against Brucella spp, C. burnetii and RVFV. Further, 280 of these were tested by PCR to identify Brucella species. Of the 16 wildlife species tested, 15 (93.8%) were seropositive for at least one of the pathogens. Mean seropositivities were 18.9% (95% CI: 15.0–23.3) for RVFV, 13.7% (95% CI: 10.3–17.7) for Brucella spp and 9.1% (95% CI: 6.3–12.5) for C. burnetii. Buffaloes (n = 269) had higher seropositivity for Brucella spp. (17.1%, 95% CI: 13.0–21.7%) and RVFV (23.4%, 95% CI: 18.6–28.6%), while giraffes (n = 36) had the highest seropositivity for C. burnetii (44.4%, 95% CI: 27.9–61.9%). Importantly, 23 of the 93 (24.7%) animals positive for at least one pathogen were co-exposed, with 25.4% (18/71) of the positive buffaloes positive for brucellosis and RVFV. On molecular analysis, Brucella DNA was detected in 46 (19.5%, CI: 14.9–24.7) samples, with 4 (8.6%, 95% CI: 2.2–15.8) being identified as B. melitensis. The Fisher’s Exact test indicated that seropositivity varied significantly within the different animal families, with Brucella (p = 0.013), C. burnetii (p = <0.001) and RVFV (p = 0.007). Location was also significantly associated (p = <0.001) with Brucella spp. and C. burnetii seropositivities. Of ~20% of Kenyan wildlife that are seropositive for Brucella spp, C. burnetii and RVFV, almost 25% indicate co-infections with the three pathogens, particularly with Brucella spp and RVFV.
Background: The effects of organochlorine pesticide (OCP) exposure on the development of human papillary thyroid cancer (PTC) are not well understood. A nested case-control study was conducted with data from the U.S. Department of Defense Serum Repository (DoDSR) cohort between 2000 and 2013 to assess associations of individual OCPs serum concentrations with PTC risk. Methods: This study included 742 histologically confirmed PTC cases (341 females, 401 males) and 742 individually-matched controls with pre-diagnostic serum samples selected from the DoDSR. Associations between categories of lipid-corrected serum concentrations of seven OCPs and PTC risk were evaluated for classical PTC and follicular PTC using conditional logistic regression, adjusted for body mass index category and military branch to compute odds ratios (OR) and 95% confidence intervals (CIs). Effect modification by sex, birth cohort, and race was examined. Results: There was no evidence of associations between most of the OCPs and PTC, overall or stratified by histological subtype. Overall, there was no evidence of an association between hexachlorobenzene (HCB) and PTC, but stratified by histological subtype HCB was associated with significantly increased risk of classical PTC (third tertile above the limit of detection (LOD) vs. <LOD, OR = 1.61, 95% CI, 1.09, 2.38; p for trend = 0.05) and significantly decreased risk of follicular variant PTC (third tertile above the limit of detection (LOD) vs. <LOD, OR = 0.38, 95% CI, 0.16, 0.91; p for trend = 0.04). Further stratified by sex, risk of classical PTC was higher for females (third tertile above LOD vs. <LOD, OR = 2.23, 95% CI: 1.23, 4.06; p-trend = 0.02) than for males (OR = 1.22, 95%CI: 0.72–2.08; p-trend = 0.56), though the test for interaction by sex was not statistically significant (p-interaction = 0.30). Similarly, β-hexachlorocyclohexane (β-HCCH) was associated with a higher risk for classical PTC for women with concentrations ≥LOD versus <LOD (OR = 1.76, 95% CI: 1.07, 2.89), while the effects were null for men. There were no consistent trends when stratified by race or birth year. Conclusions: The U.S. Environmental Protection Agency has classified HCB and other OCPs we studied here as probable human carcinogens. Our findings of increased risks for classical PTC associated with increased concentrations of HCB and β-HCCH, which were stronger among females, should be replicated in future studies of other populations.
Helicopter health monitoring systems use vibration signatures generated from damaged components to identify transmission faults. For damaged gears, these signatures relate to changes in dynamics due to the meshing of the damaged tooth. These signatures, referred to as condition indicators (CI), can perform differently when measured on different systems, such as a component test rig, or a full-scale transmission test stand, or an aircraft. These differences can result from dissimilarities in systems design and environment under dynamic operating conditions. The static structure can also filter the response between the vibration source and the accelerometer, when the accelerometer is installed on the housing. To assess the utility of static vibration transfer paths for predicting gear CI performance, measurements were taken on the NASA Glenn Spiral Bevel Gear Fatigue Test Rig. The vibration measurements were taken to determine the effect of torque, accelerometer location and gearbox design on accelerometer response. Measurements were taken at the housing and compared while impacting the gear set near mesh. These impacts were made at gear mesh to simulate gear meshing dynamics. Data measured on a helicopter gearbox installed in a static fixture were also compared to the test rig. The behavior of the structure under static conditions was also compared to CI values calculated under dynamic conditions. Results indicate that static vibration transfer path measurements can provide some insight into spiral bevel gear CI performance by identifying structural characteristics unique to each system that can affect specific CI response.
We know that the stones that fall to earth as meteorites are not representative of the full diversity of small solar system bodies, because of the peculiarities of the dynamical processes that send material into Earth-crossing paths [1] which result in severe selection biases. Thus, the bulk of the meteorites that fall are insufficient to understand the full range of early solar system processes. However, the situation is different for pebble- and smaller-sized objects that stream past the giant planets and asteroid belts into the inner solar system in a representative manner. Thus, micrometeorites and interplanetary dust particles have been exploited to permit study of objects that do not provide meteorites to earth. However, there is another population of materials that sample a larger range of small solar system bodies, but which have received little attention - pebble-sized foreign clasts in meteorites (also called xenoliths, dark inclusions, clasts, etc.). Unfortunately, most previous studies of these clasts have been misleading, in that these objects have simply been identified as pieces of CM or CI chondrites. In our work we have found this to be generally erroneous, and that CM and especially CI clasts are actually rather rare. We therefore test the hypothesis that these clasts sample the full range of small solar system bodies. We have located and obtained samples of clasts in 81 different meteorites, and have begun a thorough characterization of the bulk compositions, mineralogies, petrographies, and organic compositions of this unique sample set. In addition to the standard e-beam analyses, recent advances in technology now permit us to measure bulk O isotopic compositions, and major- though trace-element compositions of the sub-mm-sized discrete clasts. Detailed characterization of these clasts permit us to explore the full range of mineralogical and petrologic processes in the early solar system, including the nature of fluids in the Kuiper belt and the outer main asteroid belt, as revealed by the mineralogy of secondary phases.
Abstract We developed a risk assessment of human salmonellosis associated with consumption of alfalfa sprouts in the United States to evaluate the public health impact of applying treatments to seeds (0–5‐log 10 reduction in Salmonella ) and testing spent irrigation water (SIW) during production. The risk model considered variability and uncertainty in Salmonella contamination in seeds, Salmonella growth and spread during sprout production, sprout consumption, and Salmonella dose response. Based on an estimated prevalence of 2.35% for 6.8 kg seed batches and without interventions, the model predicted 76,600 (95% confidence interval (CI) 15,400 – 248,000) cases/year. Risk reduction (by 5 ‐ to 7‐fold) predicted from a 1‐log 10 seed treatment alone was comparable to SIW testing alone, and each additional 1‐log 10 seed treatment was predicted to provide a greater risk reduction than SIW testing. A 3‐log 10 or a 5‐log 10 seed treatment reduced the predicted cases/year to 139 (95% CI 33 – 448) or 1.4 (95% CI <1 – 4.5), respectively. Combined with SIW testing, a 3‐log 10 or 5‐log 10 seed treatment reduced the cases/year to 45 (95% CI 10–146) or <1 (95% CI <1 – 1.5), respectively. If the SIW coverage was less complete (i.e., less representative), a smaller risk reduction was predicted, e.g., a combined 3‐log 10 seed treatment and SIW testing with 20% coverage resulted in an estimated 92 (95% CI 22 – 298) cases/year. Analysis of alternative scenarios using different assumptions for key model inputs showed that the predicted relative risk reductions are robust. This risk assessment provides a comprehensive approach for evaluating the public health impact of various interventions in a sprout production system.
Our objective is to demonstrate an innovative method combining machine learning with comparative effectiveness research techniques and to investigate a hitherto unstudied question about the effectiveness of common prescribing patterns. For Operation Enduring Freedom/Operation Iraqi Freedom veterans with major depressive disorder, we generate pharmacotherapy pathways (of antidepressants) using process mining and machine learning. We select the medication episodes that were started at subtherapeutic doses by the first assigned primary care physician and observe the paths that those medication episodes follow. Using 2-stage least squares, we test the effectiveness of starting at a low dose and staying low for longer versus ramping up fast while balancing observable and unobservable characteristics of patients and providers through instrumental variables. We leverage predetermined provider practice patterns as instruments. We collected outpatient pharmacy data for selective serotonin reuptake inhibitors and selective norepinephrine reuptake inhibitors, patient and provider characteristics (as control variables), and the instruments for our cohort. All data were extracted for the period between 2006 and 2020. There is a statistically significant positive effect (0.68, 95% CI 0.11–1.25) of “ramping up fast” on engagement in care. When we examine the effect of “ramping up slow”, we see an insignificant negative impact on engagement in care (−0.82, 95% CI −1.89 to 0.25). As expected, the probability of drop-out also seems to have a negative effect on engagement in care (−0.39, 95% CI −0.94 to 0.17). We further validate these results by testing with medication possession ratios calculated periodically as an alternative engagement in care metric. Our findings contradict the “Start low, go slow” adage, indicating that ramping up the dose of an antidepressant faster has a significantly positive effect on engagement in care for our population.
Purpose of review: How to implement a program for MRI in patients with conditional and non-conditional (“legacy”) CIED. How to optimize safety and image quality in CMR? What the radiologists need to know: device programming, pre- and post-MRI CIED parameters. Recent findings: New Center for Medicare and Medicaid Services (CMS) guidelines have opened MRI to many patients with nonconditional devices. Newer pulse sequences for cardiac MRI (CMR) in device patients, including modified cine, late gadolinium enhancement and T1 mapping sequences, have resulted in improved image quality in device patients. We present several cases of CMR in device patients, including imaging of leadless pacemakers subcutaneous ICDs. Imaging pitfalls/artifacts in CMR interpretation are also presented. Summary: An organized institutional workflow with an established protocol involving proper patient screening, device programming, scan monitoring, and pre- and post-ICD interrogation minimizes risk in patients with conditional and non-conditional CIEDs. Although rare, significant changes in lead performance, power-on/reset, inappropriate pacing or ICD discharges and battery voltage depletion should be documented. High-quality scans with accurate scar characterization in CIED patients require the use of wideband sequences. CMS has recently acknowledged MRI as a reasonable test necessary for the diagnosis and treatment of beneficiaries with implanted CIEDs, improving the financial prospects and encouraging future developments.
Understanding the global relation between Earthquake-Induced Landslides (EQILs) and the factors contributing to their initiation is still an open topic within the geomorphological community. Accessing EQIL inventories and analyzing them concerning their potential causes is the key to explore such relation. However, each of the existing EQIL inventories has its level of completeness and associated uncertainty which makes any unified relationship which is challenging to obtain. So far, the completeness of EQIL inventories has never been clearly defined. As a result, it has never been accounted for in global EQIL predictive models. In this technical note, we propose a simple definition for the completeness of EQIL inventories. We analyze 30 digital EQIL for 21 earthquakes and develop a semi-quantitative method to estimate the completeness level, which we refer to as Completeness Index (CI). The CI results from a combination of topographic factors, ground shaking parameters, and a measure derived from landslide size statistics. The proposed CI consists of Low, Moderate, and High completeness classes which can be used to evaluate any landslide inventory. We made the whole procedure to compute the CI accessible in an ArcGIS toolbox together with a test dataset.
A new large-scale parallel multiconfigurational self-consistent field (MCSCF) implementation in the open-source NWChem computational chemistry code is presented. The generalized active space approach is used to partition large configuration interaction (CI) vectors and generate a sufficient number of batches that can be distributed to the available cores. Massively parallel CI calculations with large active spaces can be performed. The new parallel MCSCF implementation is tested for the chromium trimer and for an active space of 20 electrons in 20 orbitals, which can now routinely be performed. Unprecedented CI calculations with an active space of 22 electrons in 22 orbitals for the pentacene systems were performed and a single CI iteration calculation with an active space of 24 electrons in 24 orbitals for the chromium tetramer was possible. In conclusion, the chromium tetramer corresponds to a CI expansion of one trillion Slater determinants (914 058 513 424) and is the largest conventional CI calculation attempted up to date.
This is the final of three reports published on the results of this project. In the first report, results were presented on nineteen tests performed in the NASA Glenn Spiral Bevel Gear Fatigue Test Rig on spiral bevel gear sets designed to simulate helicopter fielded failures. In the second report, fielded helicopter HUMS data from forty helicopters were processed with the same techniques that were applied to spiral bevel rig test data. Twenty of the forty helicopters experienced damage to the spiral bevel gears, while the other twenty helicopters had no known anomalies within the time frame of the datasets. In this report, results from the rig and helicopter data analysis will be compared for differences and similarities in condition indicator (CI) response. Observations and findings using sub-scale rig failure progression tests to validate helicopter gear condition indicators will be presented. In the helicopter, gear health monitoring data was measured when damage occurred and after the gear sets were replaced at two helicopter regimes. For the helicopters or tails, data was taken in the flat pitch ground 101 rotor speed (FPG101) regime. For nine tails, data was also taken at 120 knots true airspeed (120KTA) regime. In the test rig, gear sets were tested until damage initiated and progressed while gear health monitoring data and operational parameters were measured and tooth damage progression documented. For the rig tests, the gear speed was maintained at 3500RPM, a one hour run-in was performed at 4000 in-lb gear torque, than the torque was increased to 8000 in-lbs. The HUMS gear condition indicator data evaluated included Figure of Merit 4 (FM4), Root Mean Square (RMS) or Diagnostic Algorithm 1(DA1), + 3 Sideband Index (SI3) and + 1 Sideband Index (SI1). These were selected based on their sensitivity in detecting contact fatigue damage modes from analytical, experimental and historical helicopter data. For this report, the helicopter dataset was reduced to fourteen tails and the test rig data set was reduced to eight tested gear sets. The damage modes compared were separated into three cases. For case one, both the gear and pinion showed signs of contact fatigue or scuffing damage. For case two, only the pinion showed signs of contact fatigue damage or scuffing. Case three was limited to the gear tests when scuffing occurred immediately after the gear run-in. Results of this investigation highlighted the importance of understanding the complete monitored systems, for both the helicopter and test rig, before interpreting health monitoring data. Further work is required to better define these two systems that include better state awareness of the fielded systems, new sensing technologies, new experimental methods or models that quantify the effect of system design on CI response and new methods for setting thresholds that take into consideration the variance of each system.
The diagnostics capability of micro-electro-mechanical systems (MEMS) based rotating accelerometer sensors in detecting gear tooth crack failures in helicopter main-rotor transmissions was evaluated. MEMS sensors were installed on a pre-notched OH-58C spiral-bevel pinion gear. Endurance tests were performed and the gear was run to tooth fracture failure. Results from the MEMS sensor were compared to conventional accelerometers mounted on the transmission housing. Most of the four stationary accelerometers mounted on the gear box housing and most of the CI's used gave indications of failure at the end of the test. The MEMS system performed well and lasted the entire test. All MEMS accelerometers gave an indication of failure at the end of the test. The MEMS systems performed as well, if not better, than the stationary accelerometers mounted on the gear box housing with regards to gear tooth fault detection. For both the MEMS sensors and stationary sensors, the fault detection time was not much sooner than the actual tooth fracture time. The MEMS sensor spectrum data showed large first order shaft frequency sidebands due to the measurement rotating frame of reference. The method of constructing a pseudo tach signal from periodic characteristics of the vibration data was successful in deriving a TSA signal without an actual tach and proved as an effective way to improve fault detection for the MEMS.
Here, we provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions own runners, and NVIDIA and AMD GPUs used in pre-exascale systems, (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the stewardship and advancement of community HPC codes to enable scientific discovery at scale.
Presolar grains have been identified in primitive members of all chondrite classes. The isotopic compositions of presolar grains provide probes of galactic evolution and nucleosynthesis in stars, while the abundances and characteristics of presolar grains contain a record of thermal processing in the solar system. Most of the detailed isotopic work has been done on SiC from Murchison and Orgueil, supplemented by a few studies of ordinary and enstatite chondrites. This work investigates SiC in the Colony CO3.O meteorite. SiC is present in Colony at a matrix-normalized abundance of approximately 3.7 ppm, much less than in CI chondrites and the matrixes of CM and primitive ordinary and enstatite chondrites. The abundances of SiC and other presolar grains in Colony seem to correlate with the chemical processing that produced CO3 chondrites. This implies that the known presolar grains experienced the same processing as the bulk CO3 material and assumes that the parent material was the same as that for other chondrites, including CI. That parent material is most plausibly the average material in the sun s parent molecular cloud. One test of this idea is to look for primary differences between SiC in Colony (and other meteorites) and that in CI and CM chondrites. True differences not related to thermal processing would falsify the assumption that all chondrite classes originated from the same reservoir of presolar dust.
I{esults al'e reportecl for the procluction of eeMo l'rom the accelerator-clriveu subcritical fission of a low enriohed uranir¡m (Ltju) aqì.reous solution. Phase I ol'these experiments used a 5 L r.rranyl sulfate solution with a eeMo encl-of-irracliation produotion limit of 2 Ci. The separation, recovery, and pulification of eeMo were demonstrated Lrsing the recyclecl solution. Fission product paltitioriing tl'ends will be shown for the recovery colutt'ttt, concentratiorl colurnn, and LE,U Modified Cintichem prooess. The results fi'om a 1.4 Ci oeMo production run, where the fìnal product was seut to GE Flealthcare for testing, will be highlightecl. The information gained cluring Phase ì lias signilìcantly irnpacted the clesign and implernentation of Phase ll. Phase II focuses on an end-of-irradiation ploduction of 20 Ci of eeMo and a fissior'ì power density similar to the production fàcility in a20 L LìlU uranyl sulfate solution.
Purpose: To analyze and compare the characteristics of dose distributions between Gamma Knife (GK) and CyberKnife (CK), in treating arteriovenous malformations (AVMs), and evaluate the influences on their clinical applications. Methods: Twenty four patients with AVMs treated with CK of prescribed dose (PD) of 16–25 Gy in single fraction were selected. Each patient’s CT images used for CK treatment planning with contours of targets and critical organs were exported and then loaded into the GK planning system. GK treatment plan with the same PD used in CK was generated for each patient. The metrics for dose comparison between GK and CK included conformity index (CI), gradient index (GI) of 75%, 50% and 25% of the PD, heterogeneity index (HI), volume of brain tissues covered by 10 Gy and 12 Gy, maximum dose to brainstem and beam-on time. Paired Samples t-test was used to analyze these metrics for significance (p value). Results: The CI were 0.744 ± 0.075 (GK) and 0.768 ± 0.086 (CK), p = 0.281. The GI75%, GI50%, and GI25% in GK and CK were 1.735 ± 0.100 and 2.439 ± 0.338 (p < 0.001), 3.169 ± 0.265 and 4.972 ± 0.852 (p < 0.001), and 8.650 ± 0.914 and 14.261 ± 2.476 (p < 0.001). The HI were 0.728 ± 0.072 (GK) and 0.313 ± 0.069 (CK), p < 0.001. There were significant differences both for volume of brain tissues covered by 10 Gy and 12 Gy in GK and CK (p < 0.001). GK had smaller maximum dose to brainstem. CK had shorter beam-on time. Conclusion: GK has similar dose conformity as CK, and has better normal tissue sparing but is less efficient than CK.
We provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum MonteCarlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion ofcontinuous integration (CI) targeting CPU, using GitHub Actions runners, and graphics processing units (GPU) in pre-exascalesystems, using self-hosted hardware; (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Dockercontainers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, sustainable maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the sustainability of community HPC codes and scientific discovery at scale.
The Submillimeter Wave Astronomy Satellite (SWAS) mission is dedicated to the study of star formation and interstellar chemistry. To carry out this mission, SWAS will survey dense (n(sub H2) greater than 10(exp 3) cm(exp -3)) molecular clouds within our galaxy in either the ground-state of a low-lying transition of five astrophysically important species: H2O, H2O-18, O2, CI, and CO-13. By observing these lines SWAS will: (1) test long-standing theories that predict that these species are the dominant coolants of molecular clouds during the early stages of their collapse to form stars and planets, and (2) supply heretofore missing information about the abundanceof key species central to the chemical models of dense interstellar gas. SWAS will employ two independent Schottky barrier diode mixers, passively cooled to approx. 150 K, coupled to a highly efficient 54 x 68 cm off-axis Cassegrain antenna. During its two year mission, SWAS will observe giant and dark cloud cores with the goal of detecting or setting an upper limit on the water abundance of 3 x 10(exp -6) and on th molecular oxygen abundances of 2 x 10(exp -6), both relative to H2. In addition, advantage will be taken of SWAS's relatively large beamsize of 3.2 x 4.0 arcminutes at 551 GHz and 3.6 x 4.5 arcminutes at 492 GHz to obtain large-area (approx. 1 deg x 1 deg) maps of giant and dark clouds in the CO-13 and CI lines. SWAS is scheduled for launch in mid-1995.