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result(s) for
"Stevens, James (James Paul)"
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An Empirical Background Model for the NICER X-Ray Timing Instrument
2022
Neutron Star Interior Composition Explorer has a comparatively low background rate, but it is highly variable, and its spectrum must be predicted using measurements unaffected by the science target. We describe an empirical, three-parameter model based on observations of seven pointing directions that are void of detectable sources. Two model parameters track different types of background events, while the third is used to predict a low-energy excess tied to observations conducted in sunlight. An examination of 3556 good time intervals (GTIs), averaging 570 s, yields a median rate (0.4–12 keV; 50 detectors) of 0.87 c s−1, but in 5% (1%) of cases, the rate exceeds 10 (300) c s−1. Model residuals persist at 20%–30% of the initial rate for the brightest GTIs, implying one or more missing model parameters. Filtering criteria are given to flag GTIs likely to have unsatisfactory background predictions. With such filtering, we estimate a detection limit, 1.20 c s−1 (3σ, single GTI) at 0.4–12 keV, equivalent to 3.6 × 10−12 erg cm−2 s−1 for a Crab-like spectrum. The corresponding limit for soft X-ray sources is 0.51 c s−1 at 0.3–2.0 keV, or 4.3 × 10−13 erg cm−2 s−1 for a 100 eV blackbody. These limits would be four times lower if exploratory GTIs accumulate 10 ks of data after filtering at the level prescribed for faint sources. Such filtering selects background GTIs 85% of the time. An application of the model to a 1 s timescale makes it possible to distinguish source flares from possible surges in the background.
Journal Article
New World Bats Harbor Diverse Influenza A Viruses
2013
Aquatic birds harbor diverse influenza A viruses and are a major viral reservoir in nature. The recent discovery of influenza viruses of a new H17N10 subtype in Central American fruit bats suggests that other New World species may similarly carry divergent influenza viruses. Using consensus degenerate RT-PCR, we identified a novel influenza A virus, designated as H18N11, in a flat-faced fruit bat (Artibeus planirostris) from Peru. Serologic studies with the recombinant H18 protein indicated that several Peruvian bat species were infected by this virus. Phylogenetic analyses demonstrate that, in some gene segments, New World bats harbor more influenza virus genetic diversity than all other mammalian and avian species combined, indicative of a long-standing host-virus association. Structural and functional analyses of the hemagglutinin and neuraminidase indicate that sialic acid is not a ligand for virus attachment nor a substrate for release, suggesting a unique mode of influenza A virus attachment and activation of membrane fusion for entry into host cells. Taken together, these findings indicate that bats constitute a potentially important and likely ancient reservoir for a diverse pool of influenza viruses.
Journal Article
Limnological data derived from high frequency monitoring buoys are asynchronous in a large lake
2025
Autonomous data collection is rapidly becoming an integral part of water quality monitoring, particularly for agencies looking to manage and protect aquatic ecosystems. While beneficial, it is unclear how the collection of these data can be applied in spatially complex large lakes (e.g., Laurentian Great Lakes) given the spatial heterogeneity of the ecosystem. To address this potential shortcoming in large lakes, we assessed the synchrony of sensor variables between 10 pairs of static buoys in the western basin of Lake Erie (western basin surface area = 3,282 km 2 ). Within western Lake Erie, water temperature was highly synchronous whereas dissolved oxygen, turbidity, chlorophyll and phycocyanin were asynchronous. The extent of this asynchrony was higher with increasing spatial distance between buoys. We found that between pairs of static buoys, temperature, dissolved oxygen, and turbidity all experienced decreasing correlations with increasing distance. Our results show that if researchers intend to leverage these data to answer important questions and provide real-time applications related to environmental issues like harmful algal/cyanobacterial blooms, monitoring networks need to be designed carefully with spatial complexity in mind. While autonomous data collection has many benefits, the reliance on a single or limited network of anchored monitoring buoys in large lake ecosystems has a high probability of missing important spatial features of these systems.
Journal Article
KBase: The United States Department of Energy Systems Biology Knowledgebase
2018
The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) is an open-source software and data platform designed to tackle the grand challenge of systems biology—predicting and designing biological function at scales ranging from the biomolecular to the ecological. KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large analyses on scalable computing infrastructure; and combine experimental evidence and conclusions to model plant and microbial physiology and community dynamics. The KBase platform has extensible analytical capabilities that currently include (meta)genome assembly, annotation, comparative genomics, transcriptomics, and metabolic modeling; a web-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; and a software development kit that enables the community to add functionality to the system.
Journal Article
Crystal structures of two subtype N10 neuraminidase-like proteins from bat influenza A viruses reveal a diverged putative active site
2012
Recently, we reported a unique influenza A virus subtype H17N10 from little yellow-shouldered bats. Its neuraminidase (NA) gene encodes a protein that appears to be highly divergent from all known influenza NAs and was assigned as a new subtype N10. To provide structural and functional insights on the bat H17N10 virus, X-ray structures were determined for N10 NA proteins from influenza A viruses A/little yellow-shouldered bat/Guatemala/164/2009 (GU09-164) in two crystal forms at 1.95 Å and 2.5 Å resolution and A/little yellow-shouldered bat/Guatemala/060/2010 (GU10-060) at 2.0 Å. The overall N10 structures are similar to each other and to other known influenza NA structures, with a single highly conserved calcium binding site in each monomer. However, the region corresponding to the highly conserved active site of influenza A N1-N9 NA subtypes and influenza B NA differs substantially. In particular, most of the amino acid residues required for NA activity are substituted, and the putative active site is much wider because of displacement of the 150-loop and 430-loop. These structural features and the fact that the recombinant N10 protein exhibits no, or extremely low, NA activity suggest that it may have a different function than the NA proteins of other influenza viruses. Accordingly, we propose that the N10 protein be termed an NA-like protein until its function is elucidated.
Journal Article
Self-monitoring of blood pressure in hypertension: A systematic review and individual patient data meta-analysis
by
Bosworth, Hayden B.
,
Kantola, Ilkka
,
McLaughlin, Mary Ann
in
Antihypertensive Agents - therapeutic use
,
Antihypertensives
,
Biology and Life Sciences
2017
Self-monitoring of blood pressure (BP) appears to reduce BP in hypertension but important questions remain regarding effective implementation and which groups may benefit most. This individual patient data (IPD) meta-analysis was performed to better understand the effectiveness of BP self-monitoring to lower BP and control hypertension.
Medline, Embase, and the Cochrane Library were searched for randomised trials comparing self-monitoring to no self-monitoring in hypertensive patients (June 2016). Two reviewers independently assessed articles for eligibility and the authors of eligible trials were approached requesting IPD. Of 2,846 articles in the initial search, 36 were eligible. IPD were provided from 25 trials, including 1 unpublished study. Data for the primary outcomes-change in mean clinic or ambulatory BP and proportion controlled below target at 12 months-were available from 15/19 possible studies (7,138/8,292 [86%] of randomised participants). Overall, self-monitoring was associated with reduced clinic systolic blood pressure (sBP) compared to usual care at 12 months (-3.2 mmHg, [95% CI -4.9, -1.6 mmHg]). However, this effect was strongly influenced by the intensity of co-intervention ranging from no effect with self-monitoring alone (-1.0 mmHg [-3.3, 1.2]), to a 6.1 mmHg (-9.0, -3.2) reduction when monitoring was combined with intensive support. Self-monitoring was most effective in those with fewer antihypertensive medications and higher baseline sBP up to 170 mmHg. No differences in efficacy were seen by sex or by most comorbidities. Ambulatory BP data at 12 months were available from 4 trials (1,478 patients), which assessed self-monitoring with little or no co-intervention. There was no association between self-monitoring and either lower clinic or ambulatory sBP in this group (clinic -0.2 mmHg [-2.2, 1.8]; ambulatory 1.1 mmHg [-0.3, 2.5]). Results for diastolic blood pressure (dBP) were similar. The main limitation of this work was that significant heterogeneity remained. This was at least in part due to different inclusion criteria, self-monitoring regimes, and target BPs in included studies.
Self-monitoring alone is not associated with lower BP or better control, but in conjunction with co-interventions (including systematic medication titration by doctors, pharmacists, or patients; education; or lifestyle counselling) leads to clinically significant BP reduction which persists for at least 12 months. The implementation of self-monitoring in hypertension should be accompanied by such co-interventions.
Journal Article
Pre-existing cross-reactive immunity to highly pathogenic avian influenza 2.3.4.4b A(H5N1) virus in the United States
by
Jung, Yu-Jin
,
Oshansky, Christine M.
,
Carney, Paul
in
631/250/2152/2153/1291
,
631/326/596/2562
,
692/699/255/1578
2025
The unprecedented 2.3.4.4b. A(H5N1) outbreak in dairy cattle, poultry, and spillover to humans in the United States (US) poses a major public health threat. Population immunity is a critical component of influenza pandemic risk assessment. We assessed the pre-existing cross-reactive immunity to 2.3.4.4b A(H5N1) viruses and analyzed 1794 sera from 723 people (0.5–88 yrs) in multiple US geographic regions during 2021–2024. Pre-existing neutralizing and hemagglutinin (HA)-head-binding antibodies to A(H5N1) were low, but there were substantial cross-reactive binding antibodies to N1 neuraminidase (NA) of 2.3.4.4b A(H5N1). Antibodies to group 1 HA stalk were also prevalent and increased with age. A(H1N1)pdm09 infection and influenza vaccination did not induce neutralizing antibodies to A(H5N1) viruses but induced significant rise of functional NA inhibition (NAI) antibodies to N1 of 2.3.4.4b A(H5N1), and group 1 HA stalk antibodies. Moreover, pre-pandemic stockpiled 2.3.4.4c vaccine can elicit cross-reactive neutralizing antibodies to 2.3.4.4b A(H5N1) viruses. Understanding population susceptibility is essential for pandemic preparedness.
Highly pathogenic avian influenza A H5N1 clade 2.3.4.4b virus has caused outbreaks in dairy cattle and cases in humans in the United States. Here, the authors assess levels of pre-existing cross-reactive antibodies to the epidemic virus strain in human serum samples collected in the United States.
Journal Article
Durability of Responses after SARS-CoV-2 mRNA-1273 Vaccination
by
Widge, Alicia T
,
Rouphael, Nadine G
,
Makhene, Mamodikoe
in
2019-nCoV Vaccine mRNA-1273
,
Adolescent
,
Adult
2021
Thirty-four adults received two 100-μg injections of Moderna’s mRNA SARS-CoV-2 vaccine, and serum anti–spike protein and neutralizing antibody titers were measured at day 119 — 90 days after the second injection. By three different assays, binding and neutralizing antibody titers declined slightly but remained elevated and higher than titers in convalescent plasma.
Journal Article
An mRNA Vaccine against SARS-CoV-2 — Preliminary Report
by
Peters, Etza
,
Rouphael, Nadine G
,
Makhene, Mamodikoe
in
2019-nCoV Vaccine mRNA-1273
,
Adult
,
Allergies
2020
Two inoculations with a new SARS-CoV-2 mRNA-based vaccine that encodes a protein in the coronavirus spike elicited high titers of virus-neutralizing antibody in healthy adult volunteers. Virus-specific T-cell responses were also elicited. Interim findings indicated that a dose of 100 μg per injection maximized immune response and minimized the reactogenicity of the vaccine.
Journal Article