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  • American Society of Hematology  (35,109)
  • American Geophysical Union  (28,349)
  • BioMed Central  (14,128)
  • Espoo : Geologian Tutkimuskeskus
  • Essen : Verl. Glückauf
  • 2020-2024  (350)
  • 2005-2009  (77,247)
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  • 1
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    Carbon Stocks and Potential Greenhouse Gas Production of Permafrost-Affected Active Floodplains in the Lena River Delta (2024)
    American Geophysical Union
    In:  EPIC3Journal of Geophysical Research (JGR): Biogeosciences, American Geophysical Union, 129, ISSN: 2169-8953
    Details
    Publication Date: 2024-04-19
    Description: Arctic warming increases the degradation of permafrost soils but little is known about floodplain soils in the permafrost region. This study quantifies soil organic carbon (SOC) and soil nitrogen stocks, and the potential CH4 and CO2 production from seven cores in the active floodplains in the Lena River Delta, Russia. The soils were sandy but highly heterogeneous, containing deep, organic rich deposits with 〉60% SOC stored below 30 cm. The mean SOC stocks in the top 1 m were 12.9 ± 6.0 kg C m−2. Grain size analysis and radiocarbon ages indicated highly dynamic environments with sediment re-working. Potential CH4 and CO2 production from active floodplains was assessed using a 1-year incubation at 20°C under aerobic and anaerobic conditions. Cumulative aerobic CO2 production mineralized a mean 4.6 ± 2.8% of initial SOC. The mean cumulative aerobic:anaerobic C production ratio was 2.3 ± 0.9. Anaerobic CH4 production comprised 50 ± 9% of anaerobic C mineralization; rates were comparable or exceeded those for permafrost region organic soils. Potential C production from the incubations was correlated with total organic carbon and varied strongly over space (among cores) and depth (active layer vs. permafrost). This study provides valuable information on the carbon cycle dynamics from active floodplains in the Lena River Delta and highlights the key spatial variability, both among sites and with depth, and the need to include these dynamic permafrost environments in future estimates of the permafrost carbon-climate feedback.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 2
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    Constraints on the Cryohydrological Warming of Firn and Ice in Greenland From Rayleigh Wave Ellipticity Data (2024)
    American Geophysical Union
    Details
    Publication Date: 2024-04-05
    Description: Rayleigh wave ellipticity measurements from seismic ambient noise recorded on the Greenland Ice Sheet (GrIS) show complex and anomalous behavior at wave periods sensitive to ice (T 〈 3–4 s). To understand these complex observations, we compare them with synthetic ellipticity measurements obtained from synthetic ambient noise computed for various seismic velocity and attenuation models, including surface wave overtone effects. We find that in dry snow conditions within the interior of the GrIS, to first order the anomalous ellipticity observations can be explained by ice models associated with the accumulation and densification of snow into firn. We also show that the distribution of ellipticity measurements is strongly sensitive to seismic attenuation and the thermal structure of the ice. Our results suggest that Rayleigh wave ellipticity is well suited for monitoring changes in firn properties and thermal composition of the Greenland and Antarctic ice sheets in a changing climate.
    Description: Published
    Description: e2023GL103673
    Description: OST1 Alla ricerca dei Motori Geodinamici
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Insights on long-term ecosystem changes from stable isotopes in historical squid beaks (2024)
    BioMed Central | Springer
    Details
    Publication Date: 2024-07-08
    Description: Background: Assessing the historical dynamics of key food web components is crucial to understand how climate change impacts the structure of Arctic marine ecosystems. Most retrospective stable isotopic studies to date assessed potential ecosystem shifts in the Arctic using vertebrate top predators and filter-feeding invertebrates as proxies. However, due to long life histories and specific ecologies, ecosystem shifts are not always detectable when using these taxa. Moreover, there are currently no retrospective stable isotopic studies on various other ecological and taxonomic groups of Arctic biota. To test whether climate-driven shifts in marine ecosystems are reflected in the ecology of short-living mesopredators, ontogenetic changes in stable isotope signatures in chitinous hard body structures were analysed in two abundant squids (Gonatus fabricii and Todarodes sagittatus) from the low latitude Arctic and adjacent waters, collected between 1844 and 2023. Results: We detected a temporal increase in diet and habitat-use generalism (= opportunistic choice rather than specialization), trophic position and niche width in G. fabricii from the low latitude Arctic waters. These shifts in trophic ecology matched with the Atlantification of the Arctic ecosystems, which includes increased generalization of food webs and higher primary production, and the influx of boreal species from the North Atlantic as a result of climate change. The Atlantification is especially marked since the late 1990s/early 2000s. The temporal patterns we found in G. fabricii’s trophic ecology were largely unreported in previous Arctic retrospective isotopic ecology studies. Accordingly, T. sagittatus that occur nowadays in the high latitude North Atlantic have a more generalist diet than in the XIXth century. :Conclusions Our results suggest that abundant opportunistic mesopredators with short life cycles (such as squids) are good candidates for retrospective ecology studies in the marine ecosystems, and to identify ecosystem shifts driven by climate change. Enhanced generalization of Arctic food webs is reflected in increased diet generalism and niche width in squids, while increased abundance of boreal piscivorous fishes is reflected in squids’ increased trophic position. These findings support opportunism and adaptability in squids, which renders them as potential winners of short-term shifts in Arctic ecosystems.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 4
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    Retrieving a “Weather Balloon” from the last Ice Age (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-28
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seltzer, A. M., & Tyne, R. L. Retrieving a “Weather Balloon” from the last Ice Age. AGU Advances, 3(4), (2022): e2022AV000747, https://doi.org/10.1029/2022AV000747.
    Description: “How cold was the last ice age?” is a question that paleoclimate scientists have been trying to answer for decades. Constraining the magnitude of climate change since the Last Glacial Maximum (∼20,000 years ago) can help improve our understanding of Earth's climate sensitivity and, therefore enhance our ability to predict future change (Tierney et al., 2020). Of course, there is no single answer to this question: there is spatial structure to LGM temperature change that is linked to fundamental climate system properties and processes. Consequently, paleoclimate scientists have focused on variations of this question, like “What was the latitudinal gradient of LGM temperature change?” (Chiang et al., 2003), “What was the land-sea contrast?” (Rind & Peteet, 1985) or “What was the change in ocean heat content?” (Bereiter et al., 2018). These questions inform large-scale atmospheric and oceanic circulation, the intensity of the water cycle, and planetary energy balance; the answers to these questions come from proxies like planktic and benthic foraminifera, speleothems, ice cores, pollen records, ancient groundwater, lake sediments, and glacial moraines, to name a few. In short, the paleoclimate community has developed a proxy “tool kit” equipped to map changes across the Earth's surface and into the ocean interior; but, until now, no “tool” existed for the upper atmosphere.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Sediments in sea ice drive the Canada Basin surface Mn maximum: insights from an Arctic Mn Ocean model (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-28
    Description: Author Posting. © American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 36(8), (2022): e2022GB007320, https://doi.org/10.1029/2022GB007320.
    Description: Biogeochemical cycles in the Arctic Ocean are sensitive to the transport of materials from continental shelves into central basins by sea ice. However, it is difficult to assess the net effect of this supply mechanism due to the spatial heterogeneity of sea ice content. Manganese (Mn) is a micronutrient and tracer which integrates source fluctuations in space and time while retaining seasonal variability. The Arctic Ocean surface Mn maximum is attributed to freshwater, but studies struggle to distinguish sea ice and river contributions. Informed by observations from 2009 IPY and 2015 Canadian GEOTRACES cruises, we developed a three-dimensional dissolved Mn model within a 1/12° coupled ocean-ice model centered on the Canada Basin and the Canadian Arctic Archipelago (CAA). Simulations from 2002 to 2019 indicate that annually, 87%–93% of Mn contributed to the Canada Basin upper ocean is released by sea ice, while rivers, although locally significant, contribute only 2.2%–8.5%. Downstream, sea ice provides 34% of Mn transported from Parry Channel into Baffin Bay. While rivers are often considered the main source of Mn, our findings suggest that in the Canada Basin they are less important than sea ice. However, within the shelf-dominated CAA, both rivers and sediment resuspension are important. Climate-induced disruption of the transpolar drift may reduce the Canada Basin Mn maximum and supply downstream. Other micronutrients found in sediments, such as Fe, may be similarly affected. These results highlight the vulnerability of the biogeochemical supply mechanisms in the Arctic Ocean and the subpolar seas to climatic changes.
    Description: This work was funded by the Natural Sciences and Engineering Research Council of Canada (NSERC) Climate Change and Atmospheric Research Grant: GEOTRACES (RGPCC 433848-12) and VITALS (RGPCC 433898), an NSERC Discovery Grant (RGPIN-2016-03865) to SEA, and by the University of British Columbia through a four year fellowship to BR. Computing resources were provided by Compute Canada (RRG 2648 RAC 2019, RRG 2969 RAC 2020, and RRG 1541 RAC 2021).
    Keywords: GEOTRACES ; Arctic Ocean ; Trace elements ; Canadian Arctic Archipelago ; Ocean modeling ; Micronutrients
    Repository Name: Woods Hole Open Access Server
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  • 6
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    WISTFUL: whole‐rock interpretative seismic toolbox for ultramafic lithologies (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-28
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shinevar, W., Jagoutz, O., & Behn, M. WISTFUL: whole‐rock interpretative seismic toolbox for ultramafic lithologies. Geochemistry, Geophysics, Geosystems, 23(8), (2022): e2022GC010329, https://doi.org/10.1029/2022gc010329.
    Description: To quantitatively convert upper mantle seismic wave speeds measured into temperature, density, composition, and corresponding and uncertainty, we introduce the Whole-rock Interpretative Seismic Toolbox For Ultramafic Lithologies (WISTFUL). WISTFUL is underpinned by a database of 4,485 ultramafic whole-rock compositions, their calculated mineral modes, elastic moduli, and seismic wave speeds over a range of pressure (P) and temperature (T) (P = 0.5–6 GPa, T = 200–1,600°C) using the Gibbs free energy minimization routine Perple_X. These data are interpreted with a toolbox of MATLAB® functions, scripts, and three general user interfaces: WISTFUL_relations, which plots relationships between calculated parameters and/or composition; WISTFUL_geotherms, which calculates seismic wave speeds along geotherms; and WISTFUL_inversion, which inverts seismic wave speeds for best-fit temperature, composition, and density. To evaluate our methodology and quantify the forward calculation error, we estimate two dominant sources of uncertainty: (a) the predicted mineral modes and compositions, and (b) the elastic properties and mixing equations. To constrain the first source of uncertainty, we compiled 122 well-studied ultramafic xenoliths with known whole-rock compositions, mineral modes, and estimated P-T conditions. We compared the observed mineral modes with modes predicted using five different thermodynamic solid solution models. The Holland et al. (2018, https://doi.org/10.1093/petrology/egy048) solution models best reproduce phase assemblages (∼12 vol. % phase root-mean-square error [RMSE]) and estimated wave speeds. To assess the second source of uncertainty, we compared wave speed measurements of 40 ultramafic rocks with calculated wave speeds, finding excellent agreement (Vp RMSE = 0.11 km/s). WISTFUL easily analyzes seismic datasets, integrates into modeling, and acts as an educational tool.
    Description: Funding for this study was provided by NSF Grants EAR-17-22935 (OJ) and EAR-18-44340 (MB).
    Keywords: Seismic velocity ; Seismic wave speed ; Thermodynamic modeling ; Density ; Composition ; Elastic moduli
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Accuracy and reproducibility of coral Sr/Ca SIMS timeseries in modern and fossil corals (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sayani, H., Cobb, K., Monteleone, B., & Bridges, H. Accuracy and reproducibility of coral Sr/Ca SIMS timeseries in modern and fossil corals. Geochemistry, Geophysics, Geosystems, 23(9), (2022): e2021GC010068, https://doi.org/10.1029/2021gc010068.
    Description: Coral strontium-to-calcium ratios (Sr/Ca) provide quantitative estimates of past sea surface temperatures (SST) that allow for the reconstruction of changes in the mean state and climate variations, such as the El Nino-Southern Oscillation, through time. However, coral Sr/Ca ratios are highly susceptible to diagenesis, which can impart artifacts of 1–2°C that are typically on par with the tropical climate signals of interest. Microscale sampling via Secondary Ion Mass Spectrometry (SIMS) for the sampling of primary skeletal material in altered fossil corals, providing much-needed checks on fossil coral Sr/Ca-based paleotemperature estimates. In this study, we employ a set modern and fossil corals from Palmyra Atoll, in the central tropical Pacific, to quantify the accuracy and reproducibility of SIMS Sr/Ca analyses relative to bulk Sr/Ca analyses. In three overlapping modern coral samples, we reproduce bulk Sr/Ca estimates within ±0.3% (1σ). We demonstrate high fidelity between 3-month smoothed SIMS coral Sr/Ca timeseries and SST (R = −0.5 to −0.8; p 〈 0.5). For lightly-altered sections of a young fossil coral from the early-20th century, SIMS Sr/Ca timeseries reproduce bulk Sr/Ca timeseries, in line with our results from modern corals. Across a moderately-altered section of the same fossil coral, where diagenesis yields bulk Sr/Ca estimates that are 0.6 mmol too high (roughly equivalent to −6°C artifacts in SST), SIMS Sr/Ca timeseries track instrumental SST timeseries. We conclude that 3–4 SIMS analyses per month of coral growth can provide a much-needed quantitative check on the accuracy of fossil coral Sr/Ca-derived estimates of paleotemperature, even in moderately altered samples.
    Description: We'd also like to thank Yolande Berta and Georgia Tech's Center for Nanostructure Characterization for providing access to their SEM facilities, and the Khaled bin Sultan Living Ocean Foundation and The Nature Conservancy for financial and logistical support for field excursions to Palmyra. Funding for this work was provided by the National Science Foundation (Award Numbers 1502832 and 2002458 to K.M.C) and the National Oceanic and Atmospheric Administration (Award Number: NA11OAR4310165 to K.M.C).
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Drifter observations reveal intense vertical velocity in a surface ocean front (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-03-11
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tarry, D., Ruiz, S., Johnston, T., Poulain, P., Özgökmen, T., Centurioni, L., Berta, M., Esposito, G., Farrar, J., Mahadevan, A., & Pascual, A. Drifter observations reveal intense vertical velocity in a surface ocean front. Geophysical Research Letters, 49(18), (2022): e2022GL098969, https://doi.org/10.1029/2022gl098969.
    Description: Measuring vertical motions represent a challenge as they are typically 3–4 orders of magnitude smaller than the horizontal velocities. Here, we show that surface vertical velocities are intensified at submesoscales and are dominated by high frequency variability. We use drifter observations to calculate divergence and vertical velocities in the upper 15 m of the water column at two different horizontal scales. The drifters, deployed at the edge of a mesoscale eddy in the Alboran Sea, show an area of strong convergence (urn:x-wiley:00948276:media:grl64766:grl64766-math-0001(f)) associated with vertical velocities of −100 m day−1. This study shows that a multilayered-drifter array can be an effective tool for estimating vertical velocity near the ocean surface.
    Description: This research was supported by the Office of Naval Research (ONR) Departmental Research Initiative CALYPSO under program officers Terri Paluszkiewicz and Scott Harper. The authors' ONR Grant No. are as follows: DT, SR, AM, and AP N000141613130, TMSJ N000146101612470, PP N000141812418, TO N000141812138, LRC N000141712517, and N00014191269, MB and GE N000141812782 and N000141812039, and JTF N000141812431.
    Keywords: Drifters ; Vertical velocity ; Submesoscale ; Kinematic properties ; Fronts ; Alboran Sea
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Volcano monitoring with magnetic measurements: a simulation of eruptions at axial seamount, Kilauea, Baroarbunga, and Mount Saint Helens (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-03-11
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biasi, J., Tivey, M., & Fluegel, B. Volcano monitoring with magnetic measurements: a simulation of eruptions at axial seamount, Kilauea, Baroarbunga, and Mount Saint Helens. Geophysical Research Letters, 49(17), (2022): e2022GL100006, https://doi.org/10.1029/2022GL100006.
    Description: Monitoring of active volcanic systems is a challenging task due in part to the trade-offs between collection of high-quality data from multiple techniques and the high costs of acquiring such data. Here we show that magnetic data can be used to monitor volcanoes by producing similar data to gravimetric techniques at significantly lower cost. The premise of this technique is that magma and wall rock above the Curie temperature are magnetically “transparent,” but not stationary within the crust. Subsurface movements of magma can affect the crustal magnetic field measured at the surface. We construct highly simplified magnetic models of four volcanic systems: Mount Saint Helens (1980), Axial Seamount (2015–2020), Kīlauea (2018), and Bárðarbunga (2014). In all cases, observed or inferred changes to the magmatic system would have been detectable by modern magnetometers. Magnetic monitoring could become common practice at many volcanoes, particularly in developing nations with high volcanic risk.
    Description: This work was supported by the NSF Grant No 2052963 to J. Biasi and an internal Woods Hole Oceanographic Institution grant to M. Tivey.
    Keywords: Magnetism ; Volcanic hazards ; Hawaii ; Iceland ; Volcanology ; Monitoring
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Radium inputs into the Arctic Ocean from rivers a basin‐wide estimate (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-03-11
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bullock, E., Kipp, L., Moore, W., Brown, K., Mann, P., Vonk, J., Zimov, N., & Charette, M. Radium inputs into the Arctic Ocean from rivers a basin‐wide estimate. Journal of Geophysical Research: Oceans, 127(9), (2022): e2022JC018964, https://doi.org/10.1029/2022jc018964.
    Description: Radium isotopes have been used to trace nutrient, carbon, and trace metal fluxes inputs from ocean margins. However, these approaches require a full accounting of radium sources to the coastal ocean including rivers. Here, we aim to quantify river radium inputs into the Arctic Ocean for the first time for 226Ra and to refine the estimates for 228Ra. Using new and existing data, we find that the estimated combined (dissolved plus desorbed) annual 226Ra and 228Ra fluxes to the Arctic Ocean are [7.0–9.4] × 1014 dpm y−1 and [15–18] × 1014 dpm y−1, respectively. Of these totals, 44% and 60% of the river 226Ra and 228Ra, respectively are from suspended sediment desorption, which were estimated from laboratory incubation experiments. Using Ra isotope data from 20 major rivers around the world, we derived global annual 226Ra and 228Ra fluxes of [7.4–17] × 1015 and [15–27] × 1015 dpm y−1, respectively. As climate change spurs rapid Arctic warming, hydrological cycles are intensifying and coastal ice cover and permafrost are diminishing. These river radium inputs to the Arctic Ocean will serve as a valuable baseline as we attempt to understand the changes that warming temperatures are having on fluxes of biogeochemically important elements to the Arctic coastal zone.
    Description: This study was a broad, collaborative effort that would not have been possible without contributions from numerous funding sources, including the National Science Foundation (NSF-0751525, NSF-1736277, NSF-1458305, NSF-1938873, NSF-2048067, NSF-2134865), the NERC-BMBF project CACOON [NE/R012806/1] (UKRI NERC) and BMBF-03F0806A, and an EU Starting Grant (THAWSOME-676982).
    Keywords: Radium isotopes ; Arctic Ocean ; River fluxes
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  • 11
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    Monitoring volcanic activity through combined measurements of CO2 efflux and (222Rn) and (220Rn) in soil gas: an application to Mt. Etna (Italy) (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-07
    Description: We present measurements of soil CO2 effluxes combined with soil (222Rn) and (220Rn) from two high-degassing areas on the lower flanks of Mt. Etna volcano (ZE-SV on the E flank and PAT on the SW flank). Measurements were conducted periodically from June 2006 to January 2009 in the ZE-SV area and January 2007 to January 2009 in the PAT area. The results showed significant variations in discharge activity and style. Log values of (220Rn)/(222Rn) and CO2 efflux generally follow a negative correlation, herein parameterized as the Soil Gas Disequilibrium Index (SGDI). Deviations of the SGDI from this negative correlation provide insight into variance of localized and shallow system conditions, namely rock fracturing, residual magma degassing, and near surface interactions between magmatic gases and groundwater. Statistical analysis highlighted signal anomalies, both negative and positive, that were modeled according to the physical properties and the modes of transport for each of the SGDI gas components. The revealed anomalies show correspondence with episodes of magma ascent and eruption, thereby demonstrating the potential of using the SGDI as another instrument for forecasting volcanic activity. An important strength of the SGDI, compared to other magma gas proxies like CO2 or SO2, is that the very short and very different half-lives of 222Rn (t1/2 = 3.85 days) and 220Rn (t1/2 = 55 seconds) provide unique information on the timescales of soil gas transport. Coupling the SGDI with other pre-eruptive proxies enhances the volcanological community’s response capabilities, which is critical for effective hazard mitigation.
    Description: Published
    Description: 167-202
    Description: 4V. Processi pre-eruttivi
    Keywords: Soil gases ; radon ; carbon dioxide ; volcano monitoring ; 04.08. Volcanology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
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    Can we estimate air‐sea flux of biological O2 from total dissolved oxygen? (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-03-02
    Description: Author Posting. © American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 36(9), (2022): e2021GB007145, https://doi.org/10.1029/2021gb007145.
    Description: In this study, we compare mechanistic and empirical approaches to reconstruct the air-sea flux of biological oxygen (F[O2]bio-as) by parameterizing the physical oxygen saturation anomaly (ΔO2[phy]) in order to separate the biological contribution from total oxygen. The first approach matches ΔO2[phy] to the monthly climatology of the argon saturation anomaly from a global ocean circulation model's output. The second approach derives ΔO2[phy] from an iterative mass balance model forced by satellite-based physical drivers of ΔO2[phy] prior to the sampling day by assuming that air-sea interactions are the dominant factors driving the surface ΔO2[phy]. The final approach leverages the machine-learning technique of Genetic Programming (GP) to search for the functional relationship between ΔO2[phy] and biophysicochemical parameters. We compile simultaneous measurements of O2/Ar and O2 concentration from 14 cruises to train the GP algorithm and test the validity and applicability of our modeled ΔO2[phy] and F[O2]bio-as. Among the approaches, the GP approach, which incorporates ship-based measurements and historical records of physical parameters from the reanalysis products, provides the most robust predictions (R2 = 0.74 for ΔO2[phy] and 0.72 for F[O2]bio-as; RMSE = 1.4% for ΔO2[phy] and 7.1 mmol O2 m−2 d−1 for F[O2]bio-as). We use the empirical formulation derived from GP approach to reconstruct regional, inter-annual, and decadal variability of F[O2]bio-as based on historical oxygen records. Overall, our study represents a first attempt at deriving F[O2]bio-as from snapshot measurements of oxygen, thereby paving the way toward using historical O2 data and a rapidly growing number of O2 measurements on autonomous platforms for independent insight into the biological pump.
    Description: N. Cassar was supported by the “Laboratoire d'Excellence” LabexMER (ANR-10-LABX-19) and co-funded by a grant from the French government under the program “Investissements d'Avenir.” Y. Huang was supported by grants from the China NSF (Nos. 42130401 and 42141002). Y. Huang was also partly supported by Chinese State Scholarship Fund to study at Duke University as a joint PhD student (No. 201806310052). R. Eveleth was supported by the NSF GRFP under grant (No. 1106401). D. Nicholson was supported by the NSF OCE-1129973 and OCE-1923915.
    Keywords: Air-sea gas biological oxygen flux ; Physical oxygen saturation anomaly ; Total dissolved oxygen ; Mechanistic and empirical models
    Repository Name: Woods Hole Open Access Server
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  • 13
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    Carbonation of serpentinite in creeping faults of California (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-21
    Description: Author Posting. © American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 49(15), (2022): e2022GL099185, https://doi.org/10.1029/2022gl099185.
    Description: Several large strike slip faults in central and northern California accommodate plate motions through aseismic creep. Although there is no consensus regarding the underlying cause of aseismic creep, aqueous fluids and mechanically weak, velocity-strengthening minerals appear to play a central role. This study integrates field observations and thermodynamic modeling to examine possible relationships between the occurrence of serpentinite, silica-carbonate rock, and CO2-rich aqueous fluids in creeping faults of California. Our models predict that carbonation of serpentinite leads to the formation of talc and magnesite, followed by silica-carbonate rock. While abundant exposures of silica-carbonate rock indicate complete carbonation, serpentinite-hosted CO2-rich spring fluids are strongly supersaturated with talc at elevated temperatures. Hence, carbonation of serpentinite is likely ongoing in parts of the San Andres Fault system and operates in conjunction with other modes of talc formation that may further enhance the potential for aseismic creep, thereby limiting the potential for large earthquakes.
    Description: This work was supported by National Science Foundation (NSF) grants NSF-EAR-1220280 to F. K. and J. L., NSF-EAR-1219908 to D. G., and NSF-OCE-2001728 to J. L.
    Keywords: Mineral carbonation ; Serpentinite ; Talc ; CO2 ; Aseismic creep ; San Andreas Fault
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  • 14
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    Does sea spray aerosol contribute significantly to aerosol trace element loading? a case study from the US GEOTRACES Pacific Meridional Transect (GP15) (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-21
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marsay, C. M., Landing, W. M., Umstead, D., Till, C. P., Freiberger, R., Fitzsimmons, J. N., Lanning, N. T., Shiller, A. M., Hatta, M., Chmiel, R., Saito, M., & Buck, C. S. Does sea spray aerosol contribute significantly to aerosol trace element loading? a case study from the US GEOTRACES Pacific Meridional Transect (GP15). Global Biogeochemical Cycles, 36(8), (2022): e2022GB007416. https://doi.org/10.1029/2022GB007416.
    Description: Atmospheric deposition represents a major input for micronutrient trace elements (TEs) to the surface ocean and is often quantified indirectly through measurements of aerosol TE concentrations. Sea spray aerosol (SSA) dominates aerosol mass concentration over much of the global ocean, but few studies have assessed its contribution to aerosol TE loading, which could result in overestimates of “new” TE inputs. Low-mineral aerosol concentrations measured during the U.S. GEOTRACES Pacific Meridional Transect (GP15; 152°W, 56°N to 20°S), along with concurrent towfish sampling of surface seawater, provided an opportunity to investigate this aspect of TE biogeochemical cycling. Central Pacific Ocean surface seawater Al, V, Mn, Fe, Co, Ni, Cu, Zn, and Pb concentrations were combined with aerosol Na data to calculate a “recycled” SSA contribution to aerosol TE loading. Only vanadium was calculated to have a SSA contribution averaging 〉1% along the transect (mean of 1.5%). We derive scaling factors from previous studies on TE enrichments in the sea surface microlayer and in freshly produced SSA to assess the broader potential for SSA contributions to aerosol TE loading. Maximum applied scaling factors suggest that SSA could contribute significantly to the aerosol loading of some elements (notably V, Cu, and Pb), while for others (e.g., Fe and Al), SSA contributions largely remained 〈1%. Our study highlights that a lack of focused measurements of TEs in SSA limits our ability to quantify this component of marine aerosol loading and the associated potential for overestimating new TE inputs from atmospheric deposition.
    Description: This research was supported by the National Science Foundation (NSF) grants OCE-1756103 to C. S. Buck, OCE-1756104 to W. M. Landing, OCE-1737024 to A.M. Shiller, OCE-1736906 to M. Hatta, OCE-1736875 to C. P. Till, OCE-1737167 to J. N. Fitzsimmons, and OCE-1736599 to M. Saito. In addition, N. T. Lanning was supported by the NSF Graduate Research Fellowship Program award 1746932.
    Keywords: Aerosols ; Trace elements ; GEOTRACES ; Sea spray aerosol ; Pacific Ocean
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  • 15
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    Using misorientation and weighted burgers vector statistics to understand intragranular boundary development and grain boundary formation at high temperatures (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-21
    Description: Author Posting. © American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Solid Earth 127(8), (2022): e2022JB024497, https://doi.org/10.1029/2022JB024497.
    Description: During plastic deformation, strain weakening can be achieved, in part, via strain energy reduction associated with intragranular boundary development and grain boundary formation. Grain boundaries (in 2D) are segments between triple junctions, that connect to encircle grains; every boundary segment in the encircling loop has a high (〉10°) misorientation angle. Intragranular boundaries terminate within grains or dissect grains, usually containing boundary segments with a low (〈10°) misorientation angle. We analyze electron backscatter diffraction (EBSD) data from ice deformed at −30°C (Th≈ 0.9). Misorientation and weighted Burgers vector (WBV) statistics are calculated along planar intragranular boundaries. Misorientation angles change markedly along each intragranular boundary, linking low- (〈10°) and high-angle (10–38°) segments that exhibit distinct misorientation axes and WBV directions. We suggest that these boundaries might be produced by the growth and intersection of individual intragranular boundary segments comprising dislocations with distinct slip systems. There is a fundamental difference between misorientation axis distributions of intragranular boundaries (misorientation axes mostly confined to ice basal plane) and grain boundaries (no preferred misorientation axis). These observations suggest during progressive subgrain rotation, intragranular boundaries remain crystallographically controlled up to large misorientation angles (〉〉10°). In contrast, the apparent lack of crystallographic control for grain boundaries suggests misorientation axes become randomized, likely due to the activation of additional mechanisms (such as grain boundary sliding) after grain boundary formation, linking boundary segments to encircle a grain. Our findings on ice intragranular boundary development and grain boundary formation may apply more broadly to other rock-forming minerals (e.g., olivine, quartz).
    Description: This work was supported by a NASA fund (Grant No. NNX15AM69G) to David L. Goldsby and two Marsden Funds of the Royal Society of New Zealand (Grant Nos. UOO1116, UOO052) to David J. Prior. Sheng Fan was supported by the University of Otago doctoral scholarship, the Antarctica New Zealand doctoral scholarship, a research grant from New Zealand Ministry of Business, Innovation and Employment through the Antarctic Science Platform (ANTA1801) (Grant No. ASP-023-03), and a New Zealand Antarctic Research Institute (NZARI) Early Career Researcher Seed Grant (Grant No. NZARI 2020-1-5). Open access publishing facilitated by University of Otago, as part of the Wiley – University of Otago agreement via the Council of Australian University Librarians.
    Keywords: High temperature deformation ; Misorientation ; Weighted Burgers vector ; Intragranular boundary ; Grain boundary ; Boundary geometry
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  • 16
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    Relative timing of off‐axis volcanism from sediment thickness estimates on the 8°20’N seamount chain, East Pacific Rise (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-16
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fabbrizzi, A., Parnell‐Turner, R., Gregg, P., Fornari, D., Perfit, M., Wanless, V., & Anderson, M. Relative timing of off‐axis volcanism from sediment thickness estimates on the 8°20’N seamount chain, East Pacific Rise. Geochemistry, Geophysics, Geosystems, 23(9), (2022): e2022GC010335, https://doi.org/10.1029/2022gc010335.
    Description: Volcanic seamount chains on the flanks of mid-ocean ridges record variability in magmatic processes associated with mantle melting over several millions of years. However, the relative timing of magmatism on individual seamounts along a chain can be difficult to estimate without in situ sampling and is further hampered by Ar40/Ar39 dating limitations. The 8°20’N seamount chain extends ∼170 km west from the fast-spreading East Pacific Rise (EPR), north of and parallel to the western Siqueiros fracture zone. Here, we use multibeam bathymetric data to investigate relationships between abyssal hill formation and seamount volcanism, transform fault slip, and tectonic rotation. Near-bottom compressed high-intensity radiated pulse, bathymetric, and sidescan sonar data collected with the autonomous underwater vehicle Sentry are used to test the hypothesis that seamount volcanism is age-progressive along the seamount chain. Although sediment on seamount flanks is likely to be reworked by gravitational mass-wasting and current activity, bathymetric relief and Sentry vehicle heading analysis suggest that sedimentary accumulations on seamount summits are likely to be relatively pristine. Sediment thickness on the seamounts' summits does not increase linearly with nominal crustal age, as would be predicted if seamounts were constructed proximal to the EPR axis and then aged as the lithosphere cooled and subsided away from the ridge. The thickest sediments are found at the center of the chain, implying the most ancient volcanism there, rather than on seamounts furthest from the EPR. The nonlinear sediment thickness along the 8°20’N seamounts suggests that volcanism can persist off-axis for several million years.
    Description: This work was supported by National Science Foundation awards OCE-1356610, OCE-1356822, OCE-1357150, OCE-1754419, OCE-1834797, OCE-2001314, and OCE-2001331.
    Keywords: Off-axis seamounts ; East Pacific Rise ; Sediment thickness ; Seafloor morphology ; Autonomous underwater vehicle ; Eruption history
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  • 17
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    Seismic imaging of Dante’s Domes oceanic core complex from streamer waveform inversion and reverse time migration (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-25
    Description: Author Posting. © American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Solid Earth 127(8), (2022): e2021JB023814, https://doi.org/10.1029/2021jb023814.
    Description: Early arrival traveltime tomography and full waveform inversion were conducted on downward continued streamer seismic data at Dante's Domes oceanic core complex (OCC), providing unprecedented details of shallow P wave velocity structure. Together with reverse time migration images, seafloor morphology, in situ geological samples, magnetic and gravity data, the seismic constraints are used to infer the lithological distribution along the seismic profiles. Based on the striking similarity in velocity structure beneath the corrugated domes with other OCCs and drilling results from Atlantis Massif, we confidently reconfirmed the Southern Dome as dominantly gabbroic rocks, and the Northern Dome as serpentinized peridotites. A series of isolated gabbroic bodies embedded in the diabase and basaltic layers is observed in the breakaway zone, suggesting that the initiation of Dante's Domes OCC occurred over a long period during which there were several failed attempts to form a long-lived detachment fault. This early development of the OCC probably occurred under a regime of alternating magma starvation and magma replenishment. The predominantly gabbroic section, beneath the Southern Dome and extending to termination, indicates the OCC has been created with relatively high magma flux. We also imaged distinct shallow subseafloor reflections which are also termed as D reflectors underneath the corrugated domes. The location of the D reflectors is similar to those in the Atlantis Massif, with depths well correlated with the top of exhumed gabbroic bodies and the discontinuities in the D reflectors between gabbroic bodies. Our findings contribute to the understanding of processes controlling the OCCs initiation and evolution at slow spreading ridges.
    Description: This research was supported by the National Natural Science Foundation of China (91858207), Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (GML2019ZD0205), and Guangdong Basic and Applied Basic Research Foundation (2021B1515020023). M. X. acknowledges support from Special Foundation for National Science and Technology Basic Research Program of China (2018FY100505), Guangdong NSF research team project (2017A030312002), K. C. Wong Education Foundation (GJTD-2018-13), and the Chinese Academy of Sciences (Y4SL021001, QYZDY-SSWDQC005, 133244KYSB20180029, 131551KYSB20200021, and ISEE2021PY03). J. P. C. acknowledges support from the Independent Research and Development Program at WHOI.
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  • 18
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    Spatial variability of movement, structure, and formation of Warm Core Rings in the Northwest Atlantic Slope Sea (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-25
    Description: Author Posting. © American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 127(8),(2022): e2022JC018737, https://doi.org/10.1029/2022jc018737.
    Description: Gulf Stream Warm Core Rings (WCRs) have important influences on the New England Shelf and marine ecosystems. A 10-year (2011–2020) WCR dataset that tracks weekly WCR locations and surface areas is used here to identify the rings' path and characterize their movement between 55 and 75°W. The WCR dataset reveals a very narrow band between 66 and 71°W along which rings travel almost due west along ∼39°N across isobaths – the “Ring Corridor.” Then, west of the corridor, the mean path turns southwestward, paralleling the shelfbreak. The average ring translation speed along the mean path is 5.9 cm s−1. Long-lived rings (lifespan 〉150 days) tend to occupy the region west of the New England Seamount Chain (NESC) whereas short-lived rings (lifespan 〈150 days) tend to be more broadly distributed. WCR vertical structures, analyzed using available Argo float profiles indicate that rings that are formed to the west of the NESC have shallower thermoclines than those formed to the east. This tendency may be due to different WCR formation processes that are observed to occur along different sections of the Gulf Stream. WCRs formed to the east of the NESC tend to form from a pinch-off mechanism incorporating cores of Sargasso Sea water and a perimeter of Gulf Stream water. WCRs that form to the west of the NESC, form from a process called an aneurysm. WCRs formed through aneurysms comprise water mostly from the northern half of the Gulf Stream and are smaller than the classic pinch-off rings.
    Description: AS and AG are grateful for financial support from NOAA (NA11NOS0120038), NSF (OCE-1851242 and OCE-2123283), SMAST, and UMass Dartmouth. GG was supported by NSF under grant OCE-1657853. MA was supported by NSF under grant OCE-2122726 and by ONR under grant N00014-22-1-2112.
    Keywords: Gulf Stream ; Warm core rings ; Trajectories ; Eddies ; Aneurysm ; Ring formation
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  • 19
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    Eruption rates, tempo, and stratigraphy of Paleocene flood basalts on Baffin Island, Canada (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-25
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biasi, J., Asimow, P., Horton, F., & Boyes, X. Eruption rates, tempo, and stratigraphy of Paleocene flood basalts on Baffin Island, Canada. Geochemistry, Geophysics, Geosystems, 23(9), (2022): e2021GC010172, https://doi.org/10.1029/2021gc010172.
    Description: High-temperature melting in mantle plumes produces voluminous eruptions that are often temporally coincident with mass extinctions. Paleocene Baffin Island lavas—products of early Iceland mantle plume activity—are exceptionally well characterized geochemically but have poorly constrained stratigraphy, geochronology, and eruptive tempos. To provide better geologic context, we measured seven stratigraphic sections of the volcanic deposits and collected paleomagnetic data from 38 sites in the lavas and underlying Cretaceous sediments (Quqaluit Fm.). The average paleomagnetic pole from this study does not overlap with the expected pole for a stable North American locality at 60 Ma, yet the data have sufficient dispersion to average out secular variation. After ruling out other possibilities, we find that the picrites were probably erupted during a polarity transition, over less than 5 kyr. If so, the average eruption interval was ∼67 years per flow for the thickest sequence of exposed lavas. We also calculate that the flood basalts had a minimum total volume of ∼176 km3 (excluding submerged lavas in Baffin Bay). This implies a minimum eruption rate of ∼0.035 km3 yr−1, which is similar to rates found in West Greenland lavas but less than rates found in larger flood basalts. Despite this, the Baffin and West Greenland lavas temporally correlate with the “End C27n event” (a period of ∼2°C global warming) and may be its underlying cause.
    Description: his work was supported by the National Science Foundation (award #1911699 to F. Horton and award #2052963 to J. Biasi), Woods Hole Oceanographic Institution (WHOI) Andrew W. Mellon Foundation Endowed Fund for Innovative Research, a National Geographic Society grant (#CP4-144R-18), and internal funding from the Caltech Geological and Planetary Sciences Division.
    Keywords: Baffin island ; North Atlantic ; Flood basalt ; Paleomagnetism ; Volcanology ; Secular variation
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  • 20
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    The influence of ocean topography on the upwelling of carbon in the Southern Ocean (2023)
    American Geophysical Union
    Details
    Publication Date: 2023-02-17
    Description: Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 48(19), (2021): e2021GL095088, https://doi.org/10.1029/2021GL095088.
    Description: The physical circulation of the Southern Ocean sets the surface concentration and thus air-sea exchange of CO2. However, we have a limited understanding of the three-dimensional circulation that brings deep carbon-rich waters to the surface. Here, we introduce and analyze a novel high-resolution ocean model simulation with active biogeochemistry and online Lagrangian particle tracking. We focus our attention on a subset of particles with high dissolved inorganic carbon (DIC) that originate below 1,000 m and eventually upwell into the near-surface layer (upper 200 m). We find that 71% of the DIC-enriched water upwelling across 1,000 m is concentrated near topographic features, which occupy just 33% of the Antarctic Circumpolar Current. Once particles upwell to the near-surface layer, they exhibit relatively uniform pCO2 levels and DIC decorrelation timescales, regardless of their origin. Our results show that Southern Ocean bathymetry plays a key role in delivering carbon-rich waters to the surface.
    Description: Riley X. Brady was supported by the Department of Energy's Computational Science Graduate Fellowship (DE-FG02-97ER25308), and particularly benefited from the fellowship's summer practicum at Los Alamos National Lab. Nicole S. Lovenduski and Riley X. Brady were further supported by the U.S. Department of Energy Biological and Environmental Research program (DE-SC0022243) and by the National Science Foundation (NSF-PLR 1543457; NSF-OCE 1924636; NSF-OCE 1752724; NSF-OCE 1558225). Mathew E. Maltrud and Phillip J. Wolfram were supported as part of the Energy Exascale Earth System Model (E3SM) project, funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research. This research used resources provided by the Los Alamos National Laboratory Institutional Computing Program, which is supported by the U.S. Department of Energy National Nuclear Security Administration under Contract No. 89233218CNA000001.
    Keywords: Southern Ocean ; Carbon cycle ; Upwelling ; Lagrangian modeling ; Ocean biogeochemistry ; Climate modeling
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  • 21
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    The effect of calcium supplementation on calcium and bone metabolism during load carriage in women: protocol for a randomised controlled crossover trial (2023)
    Springer | BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Military field exercises are characterised by high volumes of exercise and prolonged periods of load carriage. Exercise can decrease circulating serum calcium and increase parathyroid hormone and bone resorption. These disturbances to calcium and bone metabolism can be attenuated with calcium supplementation immediately before exercise. This randomised crossover trial will investigate the effect of calcium supplementation on calcium and bone metabolism, and bone mineral balance, during load carriage exercise in women. Methods Thirty women (eumenorrheic or using the combined oral contraceptive pill, intrauterine system, or intrauterine device) will complete two experimental testing sessions either with, or without, a calcium supplement (1000 mg). Each experimental testing session will involve one 120 min session of load carriage exercise carrying 20 kg. Venous blood samples will be taken and analysed for biochemical markers of bone resorption and formation, calcium metabolism, and endocrine function. Urine will be collected pre- and post-load carriage to measure calcium isotopes for the calculation of bone calcium balance. Discussion The results from this study will help identify whether supplementing women with calcium during load carriage is protective of bone and calcium homeostasis.
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  • 22
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    Rhythm of relationships in a social fish over the course of a full year in the wild (2023)
    BioMed Central | Springer
    Details
    Publication Date: 2024-02-07
    Description: Background: Animals are expected to adjust their social behaviour to cope with challenges in their environment. Therefore, for fish populations in temperate regions with seasonal and daily environmental oscillations, characteristic rhythms of social relationships should be pronounced. To date, most research concerning fish social networks and biorhythms has occurred in artificial laboratory environments or over confined temporal scales of days to weeks. Little is known about the social networks of wild, freely roaming fish, including how seasonal and diurnal rhythms modulate social networks over the course of a full year. The advent of high-resolution acoustic telemetry enables us to quantify detailed social interactions in the wild over time-scales sufficient to examine seasonal rhythms at whole-ecosystems scales. Our objective was to explore the rhythms of social interactions in a social fish population at various time-scales over one full year in the wild by examining high-resolution snapshots of a dynamic social network. Methods: To that end, we tracked the behaviour of 36 adult common carp, Cyprinus carpio, in a 25 ha lake and constructed temporal social networks among individuals across various time-scales, where social interactions were defined by proximity. We compared the network structure to a temporally shuffled null model to examine the importance of social attraction, and checked for persistent characteristic groups over time. Results: The clustering within the carp social network tended to be more pronounced during daytime than nighttime throughout the year. Social attraction, particularly during daytime, was a key driver for interactions. Shoaling behavior substantially increased during daytime in the wintertime, whereas in summer carp interacted less frequently, but the interaction duration increased. Therefore, smaller, characteristic groups were more common in the summer months and during nighttime, where the social memory of carp lasted up to two weeks. Conclusions: We conclude that social relationships of carp change diurnally and seasonally. These patterns were likely driven by predator avoidance, seasonal shifts in lake temperature, visibility, forage availability and the presence of anoxic zones. The techniques we employed can be applied generally to high-resolution biotelemetry data to reveal social structures across other fish species at ecologically realistic scales.
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  • 23
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    Contributions of different sea-level processes to high-tide flooding along the US coastline (2022)
    American Geophysical Union
    Details
    Publication Date: 2023-01-14
    Description: Author Posting. © American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 127(7), (2022): e2021JC018276, https://doi.org/10.1029/2021JC018276.
    Description: Coastal communities across the United States (U.S.) are experiencing an increase in the frequency of high-tide flooding (HTF). This increase is mainly due to sea-level rise (SLR), but other factors such as intra- to inter-annual mean sea level variability, tidal anomalies, and non-tidal residuals also contribute to HTF events. Here we introduce a novel decomposition approach to develop and then analyze a new database of different sea-level components. Those components represent processes that act on various timescales to contribute to HTF along the U.S. coastline. We find that the relative importance of components to HTF events strongly varies in space and time. Tidal anomalies contribute the most along the west and northeast coasts, where HTF events mostly occur in winter. Non-tidal residuals are most important along the Gulf of Mexico and mid-Atlantic coasts, where HTF events mostly occur in fall. We also quantify the minimum number of components that were required to cause HTF events in the past and how this number changed over time. The results highlight that at present, due to SLR, fewer components are needed to combine to push water levels above HTF thresholds, but tidal anomalies alone are still not sufficient to reach HTF thresholds in most locations. Finally, we explore how co-variability between different components leads to compounding effects. In some places, positive correlation between sea-level components leads to significantly more HTF events than would be expected if sea-level components were uncorrelated, whereas in other places negative correlation leads to fewer HTF events.
    Description: his work was supported by NASA's Sea Level Change Team award number 80NSSC20K1241. S.L. also acknowledges support by the China Scholarship Council (no. 201904910413) and the Ministry of Science and Technology of the People's Republic of China (grant no. 2011YQ120045).
    Description: 2023-01-14
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  • 24
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    Skillful long-lead prediction of summertime heavy rainfall in the US Midwest from sea surface salinity (2022)
    American Geophysical Union
    Details
    Publication Date: 2023-01-07
    Description: Author Posting. © American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 49(13), (2022): e2022GL098554, https://doi.org/10.1029/2022GL098554.
    Description: Summertime heavy rainfall and its resultant floods are among the most harmful natural hazards in the US Midwest, one of the world's primary crop production areas. However, seasonal forecasts of heavy rain, currently based on preseason sea surface temperature anomalies (SSTAs), remain unsatisfactory. Here, we present evidence that sea surface salinity anomalies (SSSAs) over the tropical western Pacific and subtropical North Atlantic are skillful predictors of summer time heavy rainfall one season ahead. A one standard deviation change in tropical western Pacific SSSA is associated with a 1.8 mm day−1 increase in local precipitation, which excites a teleconnection pattern to extratropical North Pacific. Via extratropical air-sea interaction and long memory of midlatitude SSTA, a wave train favorable for US Midwest heavy rain is induced. Combined with soil moisture feedbacks bridging the springtime North Atlantic salinity, the SSSA-based statistical prediction model improves Midwest heavy rainfall forecasts by 92%, complementing existing SSTA-based frameworks.
    Description: This study is supported by the NSF PREEVENTS program under ICER-1663138 (LL) and ICER-1663704 (RWS and CCU).
    Description: 2023-01-07
    Keywords: Sea surface salinity ; Midwest precipitation ; Heavy rainfall ; Long-lead prediction
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  • 25
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    Submarine groundwater discharge in the northern Bohai Sea, China: Implications for coastal carbon budgets and buffering capacity (2022)
    American Geophysical Union
    Details
    Publication Date: 2023-01-20
    Description: Author Posting. © American Geophysical Union, 2022. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Biogeosciences 127(8), (2022): e2022JG006810, https://doi.org/10.1029/2022jg006810.
    Description: Submarine groundwater discharge (SGD) has been widely recognized as an important source of dissolved nutrients in coastal waters and affects nutrient biogeochemistry. In contrast, little information is available on SGD impacts on coastal carbon budgets. Here, we assessed the SGD and associated carbon (dissolved inorganic carbon [DIC] and total alkalinity [TA]) fluxes in Liaodong Bay (the largest bay of the Bohai Sea, China) and discussed their border implications for coastal DIC budget and buffering capacity. Based on 223Ra and 228Ra mass balance models, the SGD flux was estimated to be (0.92–1.43) × 109 m3 d−1. SGD was the largest contributor of DIC, accounting for 55%–77% of the total DIC sources. The low ratio (〈1) of SGD-derived TA to DIC fluxes and negative correlation between radium isotopes and pH in seawater implied that SGD would potentially reduce seawater pH in Liaodong Bay. Combining the groundwater carbon data in Liaodong Bay with literature data, we found that the SGD-derived DIC flux off China was 4–9 times greater than those from rivers. By analyzing the TA/DIC ratios in groundwater along the Chinese coast and related carbon fluxes, SGD was thought to partially reduce the CO2 buffer capacity in receiving seawater. These results obtained at the bay scale and national scale suggest that SGD is a significant component of carbon budget and may play a critical role in modulating coastal buffering capacity and atmospheric CO2 sequestration.
    Description: his research was supported by National Natural Science Foundation of China (Grant Nos. 42130703, 42007170) and the Science, Technology and Innovation Commission of Shenzhen (Grant No. 20200925174525002.
    Description: 2023-01-20
    Keywords: Submarine groundwater discharge ; Radium isotopes ; Dissolved inorganic carbon ; Total alkalinity ; Carbon budgets ; Buffering capacity
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  • 26
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    Symbiont transmission in marine sponges: reproduction, development, and metamorphosis (2022)
    Springer | BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.
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  • 27
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    Size-differentiated export flux in different dynamical regimes in the ocean (2021)
    American Geophysical Union
    Details
    Publication Date: 2023-02-17
    Description: Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 35(3), (2021): e2020GB006764, https://doi.org/10.1029/2020GB006764
    Description: Export of Particulate Organic Carbon (POC) is mainly driven by gravitational sinking. Thus, traditionally, it is thought that larger, faster-sinking particles make up most of the POC export flux. However, this need not be the case for particles whose sinking speeds are comparable to the vertical velocities of a dynamic flow field that can influence the descent rate of particles. Particles with different settling speeds are released in two process-oriented model simulations of an upper ocean eddying flow in the Northeast Pacific to evaluate the impact of (1) ocean dynamics on the respective contribution of the different sinking-velocity classes to POC export, and (2) the particle number size-spectrum slope. The analysis reveals that the leading export mechanism changes from gravitationally driven to advectively driven as submesoscale dynamics become more active in the region. The vertical velocity associated with submesoscale dynamics enhances the contribution of slower-sinking particles to POC export flux by a factor ranging from 3 to 10, especially where the relative abundance of small particles is large (i.e., steep particle size-spectrum slope). Remineralization generally decreases the total amount of biomass exported, but its impact is weaker in dynamical regimes where submesoscale dynamics are present and export is advectively driven. In an advectively driven export regime, remineralization processes counter-intuitively enhance the role of slower-sinking particles to the point where these slower-sinking velocity classes dominate the export, therefore challenging the traditional paradigm for POC export. This study demonstrates that slow-sinking particles can be a significant contribution, and at times, even dominate the export flux.
    Description: The work was funded by NASA grant NNX16AR48 G, to complement the EXport Processes in the global Ocean from RemoTe Sensing (EXPORTS) program.
    Description: 2021-08-17
    Keywords: Export ; Flux ; Particulate organic carbon ; Sinking rates ; Submeso-scales ; Vertical velocities
    Repository Name: Woods Hole Open Access Server
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    Estimating Bioturbation From Replicated Small‐Sample Radiocarbon Ages (2021)
    American Geophysical Union
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union, 36(7), ISSN: 2572-4517
    Details
    Publication Date: 2024-06-22
    Description: Marine sedimentary records are a key archive when reconstructing past climate; however, mixing at the seabed (bioturbation) can strongly influence climate records, especially when sedimentation rates are low. By commingling the climate signal from different time periods, bioturbation both smooths climate records, by damping fast climate variations, and creates noise when measurements are made on samples containing small numbers of individual proxy carriers, such as foraminifera. Bioturbation also influences radiocarbon-based age-depth models, as sample ages may not represent the true ages of the sediment layers from which they were picked. While these effects were first described several decades ago, the advent of ultra-small-sample $^{14}$C dating now allows samples containing very small numbers of foraminifera to be measured, thus enabling us to directly measure the age-heterogeneity of sediment for the first time. Here, we use radiocarbon dates measured on replicated samples of 3-30 foraminifera to estimate age-heterogeneity for five marine sediment cores with sedimentation rates ranging from 2-30 cm kyr$^{-1}$. From their age-heterogeneities and sedimentation rates we infer mixing depths of 10-20 cm for our core sites. Our results show that when accounting for age-heterogeneity, the true error of radiocarbon dating can be several times larger than the reported measurement. We present estimates of this uncertainty as a function of sedimentation rate and the number of individuals per radiocarbon date. A better understanding of this uncertainty will help us to optimise radiocarbon measurements, construct age models with appropriate uncertainties and better interpret marine paleo records.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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    Treatment of perioperative swelling by rest, ice, compression, and elevation (RICE) without and with additional application of negative pressure (RICE+) in patients with a unilateral ankle fracture: study protocol for a monocentric, evaluator-blinded randomized controlled pilot trial (2021)
    BioMed Central | Springer
    Details
    Publication Date: 2024-02-07
    Description: Background Edema is commonly seen after surgical fixation of ankle fractures. Rest, ice, compression, and elevation (RICE) is an established combination to prevent swelling but hardly able to stimulate lymphatic resorption. Recently, an epicutaneously applied negative pressure suction apparatus (LymphaTouch®) has been introduced to stimulate lymphatic flow. While postoperative recovery, soft tissue, and osseous healing as well as functional outcome are probably linked to the amount of postoperative swelling, estimates on this relative to prevention (RICE) or prevention + stimulated resorption (RICE + ) of fluid are scarce. Methods and analysis This is a single-center, evaluator-blinded randomized pilot trial to investigate postoperative swelling in adults requiring surgical fixation of a closed unilateral ankle fracture. A total of 50 patients will be recruited and randomly assigned to RICE or RICE + prior to surgery. All patients will undergo evaluator-blinded measurements of the ankle volume the day before surgery and subsequently from the evening of the 2nd postoperative day every 24 h until discharge. RICE will be initiated right after surgery and continued until discharge from the hospital in all patients. Additional application of negative pressure therapy (RICE + ) will be initiated on the morning of the 2nd postoperative day and repeated every 24 h until the time of discharge from the hospital. Outcome measures are (i) the relative amount and the time course of the postoperative swelling, (ii) the demand for analgesic therapy (type and amount) together with the perception of pain, (iii) the rate of complications, and (iv) mobility of the ankle joint and the recovery of walking abilities during a 12-weeks follow-up period. Serum and urine samples taken prior to sugery and during postoperative recovery will allow to evaluate the ratio of naturally occurring stable calcium isotopes (δ 44/42 Ca) as a marker of skeletal calcium accrual.
    Type: Article , PeerReviewed
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    Living and dead foraminiferal assemblage from the supratidal sand Japsand, North Frisian Wadden Sea: distributional patterns and controlling factors (2021)
    Springer | BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Supratidal sands are vitally important for coastal defence in the German Wadden Sea. They are less affected by human activities than other areas as they are located far off the mainland shore, touristical and commercial activities are generally prohibited. Therefore, supratidal sands are of high ecological interest. Nevertheless, the faunal inventory and distribution pattern of microorganisms on these sands were studied very little. The composition of living and dead foraminiferal assemblages was therefore investigated along a transect from the supratidal sand Japsand up to Hallig Hooge. Both assemblages were dominated by calcareous foraminifera of which Ammonia batava was the most abundant species. Elphidium selseyense and Elphidium williamsoni were also common in the living assemblage, but Elphidium williamsoni was comparably rare in the dead assemblage. The high proportions of Ammonia batava and Elphidium selseyense in the living assemblage arose from the reproduction season that differed between species. While Ammonia batava and Elphidium selseyense just finished their reproductive cycles, Elphidium williamsoni was just about to start. This was also confirmed by the size distribution patterns of the different species. The dead assemblage revealed 20 species that were not found in the living assemblage of which some were reworked from older sediments (e.g., Bucella frigida) and some were transported via tidal currents from other areas in the North Sea (e.g., Jadammina macrescens). The living foraminiferal faunas depicted close linkages between the open North Sea and the mainland. Key species revealing exchange between distant populations were Haynesina germanica, Ammonia batava and different Elphidium species. All these species share an opportunistic behaviour and are able to inhabit a variety of different environments; hence, they well may cope with changing environmental conditions. The benthic foraminiferal association from Japsand revealed that transport mechanisms via tides and currents play a major ecological role and strongly influence the faunal composition at this site.
    Type: Article , PeerReviewed
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    Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues (2021)
    BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Background: Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding. Results: Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 °C). One hundred twelve (Pocillopora sp.) and sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context. Conclusions: Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. [MediaObject not available: see fulltext.].
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    Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis (2021)
    BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Background: Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is a key trait for aquaculture, and animal resilience under future climate change. While many enzymes and structural proteins have been identified from the shell and in mantle tissue, understanding biomieralization is impeded by a lack of fundamental knowledge of the genes and pathways involved. In adult bivalves, shells are secreted by the mantle tissue during growth, maintenance and repair, with the repair process, in particular, amenable to experimental dissection at the transcriptomic level in individual animals. Results: Gene expression dynamics were explored in the adult blue mussel, Mytilus edulis, during experimentally induced shell repair, using the two valves of each animal as a matched treatment-control pair. Gene expression was assessed using high-resolution RNA-Seq against a de novo assembled database of functionally annotated transcripts. A large number of differentially expressed transcripts were identified in the repair process. Analysis focused on genes encoding proteins and domains identified in shell biology, using a new database of proteins and domains previously implicated in biomineralization in mussels and other molluscs. The genes implicated in repair included many otherwise novel transcripts that encoded proteins with domains found in other shell matrix proteins, as well as genes previously associated with primary shell formation in larvae. Genes with roles in intracellular signalling and maintenance of membrane resting potential were among the loci implicated in the repair process. While haemocytes have been proposed to be actively involved in repair, no evidence was found for this in the M. edulis data. Conclusions: The shell repair experimental model and a newly developed shell protein domain database efficiently identified transcripts involved in M. edulis shell production. In particular, the matched pair analysis allowed factoring out of much of the inherent high level of variability between individual mussels. This snapshot of the damage repair process identified a large number of genes putatively involved in biomineralization from initial signalling, through calcium mobilization to shell construction, providing many novel transcripts for future in-depth functional analyses
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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    Gas Geochemistry at Grande Comore and Mayotte Volcanic Islands (Comoros Archipelago), Indian Ocean (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 34
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    The Climates of Earth’s Next Supercontinent: Effects of Tectonics, Rotation Rate, and Insolation (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-07-29
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 35
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    Insight Into the Early Exhumation of the Cycladic Blueschist Unit, Syros, Greece: Combined Application of Zoned Garnet Geochronology, Thermodynamic Modeling, and Quartz Elastic Barometry (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 36
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    A New Depositional Framework for Massive Iron Formations After the Great Oxidation Event (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 37
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    Body‐Wave Tomographic Imaging of the Turkana Depression: Implications for Rift Development and Plume‐Lithosphere Interactions (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 38
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    Precambrian Crystalline Basement Properties From Pressure History Matching and Implications for Induced Seismicity in the US Midcontinent (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 39
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    Focused Penetrative Plumes: A Possible Consequence of the Dissociation Transition of Post‐Perovskite at ∼0.9 TPa in Massive Rocky Super‐Earths (2021)
    American Geophysical Union
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    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 40
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    Crustal SiO 2 Content of the Emeishan Large Igneous Province and its Implications for Magma Volume and Plumbing System (2021)
    American Geophysical Union
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    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 41
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    Bias Corrected Estimation of Paleointensity (BiCEP): An Improved Methodology for Obtaining Paleointensity Estimates (2021)
    American Geophysical Union
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    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 42
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    Coral Ba/Ca Analysis Using ICP‐OES With an Ultrasonic Nebulizer (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 43
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    Cycling of CO 2 and N 2 Along the Hikurangi Subduction Margin, New Zealand: An Integrated Geological, Theoretical, and Isotopic Approach (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-09-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 44
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    Seismicity and Crustal Structure of the Southern Main Ethiopian Rift: New Evidence From Lake Abaya (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-07-28
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 45
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    Constraints on Element Mobility During Deformation Within the Seismogenic Zone, Shimanto Belt, Japan (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 46
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    Linking Intraplate Volcanism to Lithospheric Structure and Asthenospheric Flow (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 47
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    Modeling Lithospheric Deformation Using a Compressible Visco‐Elasto‐Viscoplastic Rheology and the Effective Viscosity Approach (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 48
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    The Impact of Grain Size on the Hydromechanical Behavior of Mudstones (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-07-27
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 49
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    Topside measurements at Jicamarca during the 2019 ‐ 2020 deep solar minimum (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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  • 50
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    Global impact of lightning‐produced oxidants (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-28
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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  • 51
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    Solar flare X‐ray impacts on long subionospheric VLF paths (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Print ISSN: 1542-7390
    Electronic ISSN: 1542-7390
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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  • 52
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    Subglacial channels, climate warming, and increasing frequency of Alpine glacier snout collapse (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-28
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
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  • 53
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    Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Time-lapse microscopy live-cell imaging is essential for studying the evolution of bacterial communities at single-cell resolution. It allows capturing detailed information about the morphology, gene expression, and spatial characteristics of individual cells at every time instance of the imaging experiment. The image analysis of bacterial "single-cell movies" (videos) generates big data in the form of multidimensional time series of measured bacterial attributes. If properly analyzed, these datasets can help us decipher the bacterial communities' growth dynamics and identify the sources and potential functional role of intra- and inter-subpopulation heterogeneity. Recent research has highlighted the importance of investigating the role of biological "noise" in gene regulation, cell growth, cell division, etc. Single-cell analytics of complex single-cell movie datasets, capturing the interaction of multiple micro-colonies with thousands of cells, can shed light on essential phenomena for human health, such as the competition of pathogens and benign microbiome cells, the emergence of dormant cells (“persisters”), the formation of biofilms under different stress conditions, etc. However, highly accurate and automated bacterial bioimage analysis and single-cell analytics methods remain elusive, even though they are required before we can routinely exploit the plethora of data that single-cell movies generate. Results We present visualization and single-cell analytics using R (ViSCAR), a set of methods and corresponding functions, to visually explore and correlate single-cell attributes generated from the image processing of complex bacterial single-cell movies. They can be used to model and visualize the spatiotemporal evolution of attributes at different levels of the microbial community organization (i.e., cell population, colony, generation, etc.), to discover possible epigenetic information transfer across cell generations, infer mathematical and statistical models describing various stochastic phenomena (e.g., cell growth, cell division), and even identify and auto-correct errors introduced unavoidably during the bioimage analysis of a dense movie with thousands of overcrowded cells in the microscope's field of view. Conclusions ViSCAR empowers researchers to capture and characterize the stochasticity, uncover the mechanisms leading to cellular phenotypes of interest, and decipher a large heterogeneous microbial communities' dynamic behavior. ViSCAR source code is available from GitLab at https://gitlab.com/ManolakosLab/viscar.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
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    Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.) (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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    SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Faced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise’ (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model. Results GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. ‘UK variant’) are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model. Conclusions The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Altitude of the East Asian Coastal Mountains and Their Influence on Asian Climate during Early Late Cretaceous (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Print ISSN: 2169-897X
    Electronic ISSN: 2169-8996
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Cost-effectiveness analysis of Vaborem in Carbapenem-resistant Enterobacterales (CRE) -Klebsiella pneumoniae infections in Italy (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Vaborem is a fixed dose combination of vaborbactam and meropenem with potent activity against target Carbapenem-resistant Enterobacterales (CRE) pathogens, optimally developed for Klebsiella pneumoniae carbapenemase (KPC). The study aims to evaluate the cost-effectiveness of Vaborem versus best available therapy (BAT) for the treatment of patients with CRE-KPC associated infections in the Italian setting. Methods A cost-effectiveness analysis was conducted based on a decision tree model that simulates the clinical pathway followed by physicians treating patients with a confirmed CRE-KPC infection in a 5-year time horizon. The Italian National Health System perspective was adopted with a 3% discount rate. The clinical inputs were mostly sourced from the phase 3, randomised, clinical trial (TANGO II). Unit costs were retrieved from the Italian official drug pricing list and legislation, while patient resource use was validated by a national expert. Model outcomes included life years (LYs) and quality adjusted life years (QALYs) gained, incremental costs, incremental cost-effectiveness ratio (ICER) and incremental cost-utility ratio (ICUR). Deterministic and probabilistic sensitivity analyses were also performed. Results Vaborem is expected to decrease the burden associated with treatment failure and reduce the need for chronic renal replacement therapy while costs related to drug acquisition and long-term care (due to higher survival) may increase. Treatment with Vaborem versus BAT leads to a gain of 0.475 LYs, 0.384 QALYs, and incremental costs of €3549, resulting in an ICER and ICUR of €7473/LY and €9246/QALY, respectively. Sensitivity analyses proved the robustness of the model and also revealed that the probability of Vaborem being cost-effective reaches 90% when willingness to pay is €15,850/QALY. Conclusions In the Italian setting, the introduction of Vaborem will lead to a substantial increase in the quality of life together with a minimal cost impact, therefore Vaborem is expected to be a cost-effective strategy compared to BAT.
    Electronic ISSN: 2191-1991
    Topics: Medicine , Economics
    Published by BioMed Central
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    Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be “searching followed by evaluation”, which is infeasible for long gaps, or “searching by evaluation”, which heavily relies on heuristics and thus usually yields unreliable contig paths. Results We here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps. Using simulated data from 12 species and real data from 3 species, we demonstrate the successful application of our approach in gap filling with improved accuracy and completeness of genome scaffolds. Conclusion Our approach applies a sequential Bayesian updating technique to measure the similarity between optical maps and candidate contig paths. Using this similarity to guide path searching, our approach achieves higher accuracy than the existing “searching by evaluation” strategy that relies on heuristics. Furthermore, unlike the “searching followed by evaluation” strategy enumerating all possible paths, our approach prunes the unlikely sub-paths and extends the highly-probable ones only, thus significantly increasing searching efficiency.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    Decreased plasma lipid levels in a statin-free Danish primary health care cohort between 2001 and 2018 (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Lipid levels in blood have decreased considerably during the past decades in the general population partly due to use of statins. This study aims to investigate the trends in lipid levels between 2001 and 2018 in a statin-free population from primary health care, overall and by sex and age. Methods In a cohort of 634,119 patients from general practice with no diagnoses or medical treatments that affected lipid levels of total cholesterol (TC; n = 1,574,339) between 2001 and 2018 were identified. Similarly, measurements of low-density lipoprotein cholesterol (LDL-C; n = 1,302,440), high-density lipoprotein cholesterol (HDL-C; n = 1,417,857) and triglycerides (TG; n = 1,329,477) were identified. Results Mean TC decreased from 5.64 mmol/L (95% CI: 5.63–5.65) in 2001 to 5.17 mmol/L (95% CI: 5.16–5.17) in 2018 while LDL-C decreased from 3.67 mmol/L (95% CI: 3.66–3.68) to 3.04 mmol/L (95% CI: 3.03–3.04). Women aged 70–74 years experienced the largest decreases in TC levels corresponding to a decrease of 0.7 mmol/L. The decrease in LDL-C levels was most pronounced in men ≥85 years with a decrease of 0.9 mmol/L. For both genders, TC and LDL-C levels increased with advancing age until around age 50. After menopause the women had higher TC and LDL-C levels than the men. The median (geometric mean) TG level decreased by 0.4 mmol/L from 2001 to 2008, after which it increased slightly by 0.1 mmol/L until 2018. During life the TG levels of the men were markedly higher than the women’s until around age 65–70. HDL-C levels showed no trend during the study period. Conclusions The levels of TC and LDL-C decreased considerably in a statin-free population from primary health care from 2001 to 2018. These decreases were most pronounced in the elderly population and this trend is not decelerating. For TG, levels have started to increase, after an initial decrease.
    Electronic ISSN: 1476-511X
    Topics: Biology
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    Evaluating Flat‐Crater Floor Fill Compositions and Morphologies: Insight into Formation Processes (2021)
    American Geophysical Union
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    Publication Date: 2021-10-30
    Print ISSN: 2169-9097
    Electronic ISSN: 2169-9100
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Seed priming with proline improved photosystem II efficiency and growth of wheat (Triticum aestivum L.) (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Proline can promote growth of plants by increasing photosynthetic activity under both non-stress and abiotic stress conditions. However, its role in non-stressed conditions is least studied. An experiment was conducted to assess as to whether increase in growth of wheat due to seed priming with proline under non-stress condition was associated with proline-induced changes in photosystem II (PSII) activity. Seeds of four wheat varieties (S-24, Sehar-06, Galaxy-13, and Pasban-90) were primed with different concentrations of proline (0, 5, 15 and 25 mM) for 12 h and allowed to grow under normal conditions. Biomass accumulation and photosynthetic performance, being two most sensitive features/indicators of plant growth, were selected to monitor proline modulated changes. Results Seed priming with proline increased the fresh and dry weights of shoots and roots, and plant height of all four wheat varieties. Maximum increase in growth attributes was observed in all four wheat varieties at 15 mM proline. Maximum growth improvement due to proline was found in var. Galaxy-13, whereas the reverse was true for S-24. Moreover, proline treatment changed the Fo, Fm, Fv/Fo, PIABS, PITot in wheat varieties indicating changes in PSII activity. Proline induced changes in energy fluxes for absorption, trapping, electron transport and heat dissipation per reaction center indicated that var. Galaxy-13 had better ability to process absorbed light energy through photosynthetic machinery. Moreover, lesser PSII efficiency in var. S-24 was due to lower energy flux for electron transport and greater energy flux for heat dissipation. This was further supported by the fact that var. S-24 had disturbance at acceptor side of PSI as reflected by reduction in ΔVIP, probability and energy flux for electron transport at the PSI end electron acceptors. Conclusion Seed priming with proline improved the growth of wheat varieties, which depends on type of variety and concentration of proline applied. Seed priming with proline significantly changed the PSII activity in wheat varieties, however, its translation in growth improvement depends on potential of processing of absorbed light energy by electron acceptors of electron transport chain, particularly those present at PSI end.
    Electronic ISSN: 1471-2229
    Topics: Biology
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    Observations and Modeling of Strong Thermospheric Winds at High Latitudes and Their Impact on the Lower Thermosphere (2021)
    American Geophysical Union
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    Publication Date: 2021-10-29
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Bifurcated Current Sheets in Mercury’s Magnetotail: Observations and Implications (2021)
    American Geophysical Union
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    Publication Date: 2021-10-29
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Non‐Marine Sources Contribute to Aerosol Methanesulfonate Over Coastal Seas (2021)
    American Geophysical Union
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    Publication Date: 2021-10-29
    Print ISSN: 2169-897X
    Electronic ISSN: 2169-8996
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Coseismic and Early Postseismic Deformation Due to the 2021 M7.4 Maduo (China) Earthquake (2021)
    American Geophysical Union
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    Publication Date: 2021-10-29
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Toward Improving Point‐Source Moment‐Tensor Inference by Incorporating 1D Earth Model’s Uncertainty: Implications for the Long Valley Caldera Earthquakes (2021)
    American Geophysical Union
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    Publication Date: 2021-10-30
    Print ISSN: 2169-9313
    Electronic ISSN: 2169-9356
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Clinical characteristics of cardiovascular patients with extremely low levels of high-density lipoprotein cholesterol (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Extremely low levels of high-density lipoprotein cholesterol (HDL-C) are related to high cardiovascular mortality. The underlying mechanism is not well known. This research aims to study the clinical characteristics of cardiovascular patients with extremely low levels of HDL-C. Methods All cardiovascular patients in a single Chinese cardiology center that were admitted from January to December 2019 were reviewed. The clinical characteristics of those with HDL-C
    Electronic ISSN: 1476-511X
    Topics: Biology
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    A Plate–Mantle Convection System in the West Pacific Revealed by Tertiary Ultramafic–Mafic Volcanic Rocks in Southeast China (2021)
    American Geophysical Union
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    Publication Date: 2021-10-30
    Electronic ISSN: 2333-5084
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Identification of defense related gene families and their response against powdery and downy mildew infections in Vitis vinifera (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Grapevine (Vitis vinifera) productivity has been severely affected by various bacterial, viral and fungal diseases worldwide. When a plant is infected with the pathogen, various defense mechanisms are subsequently activated in plants at various molecular levels. Thus, for substantiating the disease control in an eco-friendly way, it is essential to understand the molecular mechanisms governing pathogen resistance in grapes. Results In our study, we performed genome-wide identification of various defensive genes expressed during powdery mildew (PM) and downy mildew (DM) infections in grapevine. Consequently, we identified 6, 21, 2, 5, 3 and 48 genes of Enhanced Disease Susceptibility 1 (EDS1), Non-Race-specific Disease Resistance (NDR1), Phytoalexin deficient 4 (PAD4), Nonexpressor of PR Gene (NPR), Required for Mla-specified resistance (RAR) and Pathogenesis Related (PR), respectively, in the grapevine genome. The phylogenetic study revealed that V. vinifera defensive genes are evolutionarily related to Arabidopsis thaliana. Differential expression analysis resulted in identification of 2, 4, 7, 2, 4, 1 and 7 differentially expressed Nucleotide-binding leucine rich repeat receptor (NLR), EDS1, NDR1, PAD4, NPR, RAR1 and PR respectively against PM infections and 28, 2, 5, 4, 1 and 19 differentially expressed NLR, EDS1, NDR1, NPR, RAR1 and PR respectively against DM infections in V. vinifera. The co-expression study showed the occurrence of closely correlated defensive genes that were expressed during PM and DM stress conditions. Conclusion The PM and DM responsive defensive genes found in this study can be characterized in future for impelling studies relaying fungal and oomycete resistance in plants, and the functionally validated genes would then be available for conducting in-planta transgenic gene expression studies for grapes.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    A drug repositioning algorithm based on a deep autoencoder and adaptive fusion (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Drug repositioning has caught the attention of scholars at home and abroad due to its effective reduction of the development cost and time of new drugs. However, existing drug repositioning methods that are based on computational analysis are limited by sparse data and classic fusion methods; thus, we use autoencoders and adaptive fusion methods to calculate drug repositioning. Results In this study, a drug repositioning algorithm based on a deep autoencoder and adaptive fusion was proposed to mitigate the problems of decreased precision and low-efficiency multisource data fusion caused by data sparseness. Specifically, a drug is repositioned by fusing drug-disease associations, drug target proteins, drug chemical structures and drug side effects. First, drug feature data integrated by drug target proteins and chemical structures were processed with dimension reduction via a deep autoencoder to characterize feature representations more densely and abstractly. Then, disease similarity was computed using drug-disease association data, while drug similarity was calculated with drug feature and drug-side effect data. Predictions of drug-disease associations were also calculated using a top-k neighbor method that is commonly used in predictive drug repositioning studies. Finally, a predicted matrix for drug-disease associations was acquired after fusing a wide variety of data via adaptive fusion. Based on experimental results, the proposed algorithm achieves a higher precision and recall rate than the DRCFFS, SLAMS and BADR algorithms with the same dataset. Conclusion The proposed algorithm contributes to investigating the novel uses of drugs, as shown in a case study of Alzheimer's disease. Therefore, the proposed algorithm can provide an auxiliary effect for clinical trials of drug repositioning.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    LongStitch: high-quality genome assembly correction and scaffolding using long reads (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    Mesenchymal stem cells-derived exosomes for drug delivery (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Exosomes are extracellular vesicles secreted by various cells, mainly composed of lipid bilayers without organelles. In recent years, an increasing number of researchers have focused on the use of exosomes for drug delivery. Targeted drug delivery in the body is a promising method for treating many refractory diseases such as tumors and Alzheimer's disease (AD). Finding a suitable drug delivery carrier in the body has become a popular research today. In various drug delivery studies, the exosomes secreted by mesenchymal stem cells (MSC-EXOs) have been broadly researched due to their immune properties, tumor-homing properties, and elastic properties. While MSC-EXOs have apparent advantages, some unresolved problems also exist. This article reviews the studies on MSC-EXOs for drug delivery, summarizes the characteristics of MSC-EXOs, and introduces the primary production and purification methods and drug loading methods to provide solutions for existing problems and suggestions for future studies.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
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    Effects of dyslipidemia on E antigen seroconversion of patients with chronic hepatitis B treated by nucleoside (acid) analogs (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background The prevalence of dyslipidemia in China is increasing annually. Current studies suggest that dyslipidemia affects the antiviral efficacy of hepatitis C virus (HCV) therapies, while recent studies suggest that serum lipids influence the response rates of chronic hepatitis B (CHB) patients receiving PEGylated interferon-alpha (Peg IFN-α) treatment. However, the role of dyslipidemia in the efficacy of nucleoside (acid) analogues (NAs) in CHB patients remains unclear. Methods From January 2010 to December 2013, data from 179 treatment-naive patients with CHB who were hepatitis B e antigen (HBeAg)-positive and had visited the first affiliated hospital of Wenzhou Medical University were assessed. Of these patients, 68 were assigned to the dyslipidemia group (diagnosed with CHB complicated with dyslipidemia) and 111 to the normolipidemic group. The following 3 treatment strategies were performed for all CHB patients over a 5-year period: lamivudine (LAM) plus adefovir dipivoxil (ADV) combination therapy, telbivudine (LdT) monotherapy, and entecavir (ETV) monotherapy. Serum assessments, blood biochemistry, HBV serological markers, HBV DNA before treatment and HBeAg serological conversion and virological responses at different timepoints after treatment were compared between the two groups. Measurement data were compared by τ tests and enumeration data by χ2 tests. Correlation analysis was performed using binary logistic regression analysis. Results The rates of HBeAg seroconversion in the dyslipidemia group at years 1, 2, 3, and 4 were 10.3, 13.2, 17.6, and 22.1%, respectively, which were not significantly lower than those of the normolipidemic group (11.7, 16.2, 18.0 and 33.3%; χ2 = 0.085, 0.293, 0.004, and 2.601, respectively; Ρ 〉 0.05). However, the rates of HBeAg seroconversion in the dyslipidemia group were significantly lower than those in the normolipidemic group at year 5 (27.9% vs. 43.2%, χ2 = 4.216, Ρ 
    Electronic ISSN: 1476-511X
    Topics: Biology
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    Population variation alters aggression-associated oxytocin and vasopressin expressions in brains of Brandt’s voles in field conditions (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Density-dependent change in aggressive behavior contributes to the population regulation of many small rodents, but the underlying neurological mechanisms have not been examined in field conditions. We hypothesized that crowding stress and aggression-associated oxytocin (OT) and arginine vasopressin (AVP) in specific regions of the brain may be closely related to aggressive behaviors and population changes of small rodents. We analyzed the association of OT and AVP expression, aggressive behavior, and population density of Brandt’s voles in 24 large semi-natural enclosures (0.48 ha each) in Inner Mongolia grassland. We tested the effects of population density on the OT/AVP system and aggressive behavior by experimentally manipulating populations of Brandt’s voles in the grassland enclosures. High density was positively and significantly associated with more aggressive behavior, and increased expression of mRNA and protein of AVP and its receptor, but decreased expression of mRNA and protein of OT and its receptor in specific brain regions of the voles. Our study suggests that changes in OT/AVP expression are likely a result of the increased psychosocial stress that these voles experience during overcrowding, and thus the OT/AVP system can be used as indicators of density-dependent stressors in Brandt’s voles.
    Electronic ISSN: 1742-9994
    Topics: Biology
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    Microseismicity appears to outline highly coupled regions on the Central Chile megathrust (2021)
    American Geophysical Union
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    Publication Date: 2021-10-30
    Print ISSN: 2169-9313
    Electronic ISSN: 2169-9356
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Assessing the suitability of general practice electronic health records for clinical prediction model development: a data quality assessment (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background The use of general practice electronic health records (EHRs) for research purposes is in its infancy in Australia. Given these data were collected for clinical purposes, questions remain around data quality and whether these data are suitable for use in prediction model development. In this study we assess the quality of data recorded in 201,462 patient EHRs from 483 Australian general practices to determine its usefulness in the development of a clinical prediction model for total knee replacement (TKR) surgery in patients with osteoarthritis (OA). Methods Variables to be used in model development were assessed for completeness and plausibility. Accuracy for the outcome and competing risk were assessed through record level linkage with two gold standard national registries, Australian Orthopaedic Association National Joint Replacement Registry (AOANJRR) and National Death Index (NDI). The validity of the EHR data was tested using participant characteristics from the 2014–15 Australian National Health Survey (NHS). Results There were substantial missing data for body mass index and weight gain between early adulthood and middle age. TKR and death were recorded with good accuracy, however, year of TKR, year of death and side of TKR were poorly recorded. Patient characteristics recorded in the EHR were comparable to participant characteristics from the NHS, except for OA medication and metastatic solid tumour. Conclusions In this study, data relating to the outcome, competing risk and two predictors were unfit for prediction model development. This study highlights the need for more accurate and complete recording of patient data within EHRs if these data are to be used to develop clinical prediction models. Data linkage with other gold standard data sets/registries may in the meantime help overcome some of the current data quality challenges in general practice EHRs when developing prediction models.
    Electronic ISSN: 1472-6947
    Topics: Computer Science , Medicine
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    Risk factors for development of nephropathy in patients with a diabetic Charcot foot (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Objective Charcot foot is a rare complication to neuropathy and can cause severe foot deformities and ulcerations, which often require prolonged antibiotical treatment. The objective of this retrospective study was to investigate whether this treatment is associated to impaired renal function. Results In total, 163 patients were included, of whom 105 (64%) had received β-lactam antibiotics for a mean total duration of 13.0 months. There was a significant increase in the urine albumin/creatinine ratio in the group that received antibiotics (p = 0.017), and the use of antibiotics was associated to a subsequent diagnosis of nephropathy (p = 0.01). Patients treated with antibiotics had a 21.9% risk of developing subsequent nephropathy versus 5.2% for patients not treated with antibiotics. We suggest increased awareness on signs of nephropathy in patients with severe Charcot foot.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
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    Alien balsams, strawberries and their pollinators in a warmer world (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Strawberries are a common crop whose yield success depends on the availability of pollinators. Invasive alien plants, such as Impatiens glandulifera and I. parviflora, are also attractive for bees and hoverflies, respectively, and occur in close proximity to strawberry cultivation areas. The aim of the study was to test whether alien plants may decrease pollination of strawberry cultivation. However, even if the pollinators are abundant, efficiency of their pollination may decrease as a result of revisits of flowers that were already probed. It is addressed by pollinators by scent marking. Moreover, such revisits can be determined by nectar replenishment, which may occur rapidly in nectar-rich flowers. We studied revisits to I. glandulifera by bumblebees and defined the factors that influence the probability of revisits (air temperature; pollinator species; family caste and size; flower area; sun radiation; and time of day). Results We found that the two alien species decreased the number of pollinators visiting strawberries. Apoidea, Bombini and Syrphidae significantly decreased on Fragaria × ananassa when alien Impatiens were present. We also revealed the influence of increasing air temperature on bumblebee foraging, which was particularly significant for female workers. At very high temperatures (〉 37°C), bumblebee males revisited probed flowers less often than female workers. Conclusions Our results demonstrate that in experimental conditions attractive alien species decrease pollination of strawberries, which may negatively affect production of this crop. Although the results have not been verified in real-life strawberry fields yet, we recommend that alien plant species that share the same pollinators and occur in close proximity of strawberries are controlled. Moreover, we found that revisits of probed flowers may weaken feeding efficiency of bumblebees. If revisits are not induced by nectar replenishment, then global warming may pose a serious threat to the survival of colonies, which may have consequences also for the plants that attract them, e.g., for strawberries.
    Electronic ISSN: 1471-2229
    Topics: Biology
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    Gender representation in food and beverage print advertisements found in corner stores around schools in Peru and Guatemala (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Objective The objective of this study is to assess gender representation in food and beverage print advertisements. Results The study follows a quantitative descriptive approach. Using a content analysis technique, we assessed the gender representation in 200 food and beverage print advertisements found in corner stores located in four areas around schools in Lima, Peru, and Guatemala City, Guatemala (100 advertisements per country). A total of 36% of the print advertisements exhibited a male main character for the case of Guatemala, while in Peru 14% of the print advertisements presented a male main character. Furthermore, in Guatemala, 22% of the main characters were male animated characters. Moreover, 27% of the print advertisements in Guatemala and 17%, in Peru were visually male-oriented. Overall, male characters appeared alongside sports references and in varied settings, whereas female characters were usually holding or consuming the product. In conclusion, although the majority of variables used to assess the representation of gender in food and beverage print advertisements were gender-neutral, those showing gender representation were mostly male-oriented. Despite its limited findings, the study provides evidence for the formulation of public policies and educational content aimed to protect children’s and adolescents’ health from the effects of food marketing.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
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    Mitochondrial dysfunction, UPRmt signaling, and targeted therapy in metastasis tumor (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: In modern research, mitochondria are considered a more crucial energy plant in cells. Mitochondrial dysfunction, including mitochondrial DNA (mtDNA) mutation and denatured protein accumulation, is a common feature of tumors. The dysfunctional mitochondria reprogram molecular metabolism and allow tumor cells to proliferate in the hostile microenvironment. One of the crucial signaling pathways of the mitochondrial dysfunction activation in the tumor cells is the retrograde signaling of mitochondria-nucleus interaction, mitochondrial unfolded protein response (UPRmt), which is initiated by accumulation of denatured protein and excess ROS production. In the process of UPRmt, various components are activitated to enhance the mitochondria-nucleus retrograde signaling to promote carcinoma progression, including hypoxia-inducible factor (HIF), activating transcription factor ATF-4, ATF-5, CHOP, AKT, AMPK. The retrograde signaling molecules of overexpression ATF-5, SIRT3, CREB, SOD1, SOD2, early growth response protein 1 (EGR1), ATF2, CCAAT/enhancer-binding protein-d, and CHOP also involved in the process. Targeted blockage of the UPRmt pathway could obviously inhibit tumor proliferation and metastasis. This review indicates the UPRmt pathways and its crucial role in targeted therapy of metastasis tumors.
    Electronic ISSN: 2045-3701
    Topics: Biology
    Published by BioMed Central
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    Synergistic stimulation of osteoblast differentiation of rat mesenchymal stem cells by leptin and 25(OH)D3 is mediated by inhibition of chaperone-mediated autophagy (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Vitamin D is important for the mineralization of bones by stimulating osteoblast differentiation of bone marrow mesenchymal stem cells (BMMSCs). BMMSCs are a target of vitamin D action, and the metabolism of 25(OH)D3 to biologically active 1α,25(OH)2D3 in BMMSCs promotes osteoblastogenesis in an autocrine/paracrine manner. Our previous study with human BMMSCs showed that megalin is required for the 25(OH)D3-DBP complex to enter cells and for 25(OH)D3 to stimulate osteoblast differentiation in BMMSCs. Furthermore, we reported that leptin up-regulates megalin in those cells. Leptin is a known inhibitor of PI3K/AKT-dependent chaperone-mediated autophagy (CMA). In this study, we tested the hypothesis that leptin acts synergistically with 25(OH)D3 to promote osteoblastogenesis in rat BMMSCs by a mechanism that entails inhibition of PI3K/AKT-dependent CMA. Methods BMMSCs were isolated from rat bone marrow (4-week-old male SD rats); qRT-PCR and western immunoblots or immunofluorescence were used to evaluate the expression of megalin, ALP, COL1A1, RUNX2, OSX, OSP, and CMA in rBMMSCs. The osteoblast differentiation was evaluated by ALP activity, ALP staining, and calcium deposition. The viability of rBMMSCs was assessed with the CCK-8 kit. Biosynthesis of 1α,25(OH)2D3 was measured by a Rat 1α,25(OH)2D3 ELISA Kit. Results The combination of leptin and 25(OH)D3 treatment significantly enhanced osteoblast differentiation as shown by ALP activity, ALP staining, and calcium deposition, the expression of osteogenic genes ALP, COL1A1, RUNX2, OSX, and OSP by qRT-PCR and western immunoblots in rBMMSCs. Leptin enhanced the expression of megalin and synthesis of 1α,25(OH)2D3 in rBMMSCs. Our data showed that leptin inhibited CMA activity of rBMMSCs by activating PI3K/AKT signal pathway; the ability of leptin to enhance 25(OH)D3 promoted osteoblast differentiation of rBMMSCs was weakened by the PI3K/AKT signal pathway inhibitor. Conclusions Our data reveal the mechanism by which leptin and 25(OH)D3 promote osteoblast differentiation in rBMMSCs. Leptin promoted the expression of megalin by inhibiting CMA, increased the utilization of 25(OH)D3 by rBMMSCs, and enhanced the ability of 25(OH)D3 to induce osteoblast differentiation of rBMMSCs. PI3K/AKT is at least partially involved in the regulation of CMA. These data indicate the importance of megalin in BMMSCs for vitamin D’s role in skeletal health.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
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    Wharton’s jelly mesenchymal stem cells embedded in PF-127 hydrogel plus sodium ascorbyl phosphate combination promote diabetic wound healing in type 2 diabetic rat (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Diabetic cutaneous ulcers (DCU) are a complication of diabetes with diabetic foot ulcers being the most common, and the wounds are difficult to heal, increasing the risk of bacterial infection. Cell-based therapy utilizing mesenchymal stem cells (MSCs) is currently being investigated as a therapeutic avenue for both chronic diabetic ulcers and severe burns. Wharton’s jelly mesenchymal stem cell (WJMSC) with PF-127 hydrogel and sodium ascorbyl phosphate (SAP) improved skin wound healing in mice. Whether this combination strategy is helpful to diabetic ulcers wound healing remains to be explored. Methods Firstly, the WJMSCs embedded in PF-127 and SAP combination were transplanted onto excisional cutaneous wound bed in type 2 diabetic Sprague Dawley (SD) rats. Two weeks after transplantation, the skin tissue was collected for histological and immunohistochemical analysis. Further, overexpressing-EGFP WJMSCs were performed to investigate cell engraftment in the diabetic cutaneous ulcer. The apoptosis of WJMSCs which encapsulated with combination of PF-127 and SAP was detected by TUNEL fluorescence assay and RT-PCR in vitro. And the mitochondrial damage induced by oxidative stress assessed by MitoTracker and CMH2DCFDA fluorescence assay. Results In diabetic cutaneous wound rat model, PF-127 plus SAP-encapsulated WJMSCs transplantation promoted diabetic wound healing, indicating improving dermis regeneration and collagen deposition. In diabetic wound healing, less pro-inflammatory M1 macrophages, more anti-inflammatory M2 tissue-healing macrophages, and neovascularization were observed in PF-127 + SAP + WJMSCs group compared with other groups. SAP supplementation alleviated the apoptosis ratio of WJMSCs embedded in the PF-127 in vitro and promoted cell survival in vivo. Conclusion PF-127 plus SAP combination facilitates WJMSCs-mediated diabetic wound healing in rat through promoting cell survival, the macrophage transformation, and angiogenesis. Our findings may potentially provide a helpful therapeutic strategy for patients with diabetic cutaneous ulcer.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
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    Ex vivo expansion and characterization of human corneal endothelium for transplantation: a review (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: The corneal endothelium plays a key role in maintaining corneal transparency. Its dysfunction is currently treated with penetrating or lamellar keratoplasty. Advanced cell therapy methods seek to address the persistent global deficiency of donor corneas by enabling the renewal of the endothelial monolayer with tissue-engineered grafts. This review provides an overview of recently published literature on the preparation of endothelial grafts for transplantation derived from cadaveric corneas that have developed over the last decade (2010–2021). Factors such as the most suitable donor parameters, culture substrates and media, endothelial graft storage conditions, and transplantation methods are discussed. Despite efforts to utilize alternative cellular sources, such as induced pluripotent cells, cadaveric corneas appear to be the best source of cells for graft preparation to date. However, native endothelial cells have a limited natural proliferative capacity, and they often undergo rapid phenotype changes in ex vivo culture. This is the main reason why no culture protocol for a clinical-grade endothelial graft prepared from cadaveric corneas has been standardized so far. Currently, the most established ex vivo culture protocol involves the peel-and-digest method of cell isolation and cell culture by the dual media method, including the repeated alternation of high and low mitogenic conditions. Culture media are enriched by additional substances, such as signaling pathway (Rho-associated protein kinase, TGF-β, etc.) inhibitors, to stimulate proliferation and inhibit unwanted morphological changes, particularly the endothelial-to-mesenchymal transition. To date, this promising approach has led to the development of endothelial grafts for the first in-human clinical trial in Japan. In addition to the lack of a standard culture protocol, endothelial-specific markers are still missing to confirm the endothelial phenotype in a graft ready for clinical use. Because the corneal endothelium appears to comprise phenotypically heterogeneous populations of cells, the genomic and proteomic expression of recently proposed endothelial-specific markers, such as Cadherin-2, CD166, or SLC4A11, must be confirmed by additional studies. The preparation of endothelial grafts is still challenging today, but advances in tissue engineering and surgery over the past decade hold promise for the successful treatment of endothelial dysfunctions in more patients worldwide.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
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    Post‐wildfire Generation of Debris‐flow Slurry by Rill Erosion on Colluvial Hillslopes (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-30
    Print ISSN: 2169-9003
    Electronic ISSN: 2169-9011
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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  • 85
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    Neighborhoods Are Feeling the Heat of Climate Change (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Description: It’s no secret there are disparities in exposure to climate change’s effects. A new study zeroes in on the demographics of neighborhoods subjected to the hottest temperatures.
    Print ISSN: 0096-3941
    Electronic ISSN: 2324-9250
    Topics: Geosciences
    Published by American Geophysical Union
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    Activation of adult mammalian retinal stem cells in vivo via antagonism of BMP and sFRP2 (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background The adult mammalian retina does not have the capacity to regenerate cells lost due to damage or disease. Therefore, retinal injuries and blinding diseases result in irreversible vision loss. However, retinal stem cells (RSCs), which participate in retinogenesis during development, persist in a quiescent state in the ciliary epithelium (CE) of the adult mammalian eye. Moreover, RSCs retain the ability to generate all retinal cell types when cultured in vitro, including photoreceptors. Therefore, it may be possible to activate endogenous RSCs to induce retinal neurogenesis in vivo and restore vision in the adult mammalian eye. Methods To investigate if endogenous RSCs can be activated, we performed combinatorial intravitreal injections of antagonists to BMP and sFRP2 proteins (two proposed mediators of RSC quiescence in vivo), with or without growth factors FGF and Insulin. We also investigated the effects of chemically-induced N-methyl-N-Nitrosourea (MNU) retinal degeneration on RSC activation, both alone and in combination withthe injected factors. Further, we employed inducible Msx1-CreERT2 genetic lineage labeling of the CE followed by stimulation paradigms to determine if activated endogenous RSCs could migrate into the retina and differentiate into retinal neurons. Results We found that in vivo antagonism of BMP and sFRP2 proteins induced CE cells in the RSC niche to proliferate and expanded the RSC population. BMP and sFRP2 antagonism also enhanced CE cell proliferation in response to exogenous growth factor stimulation and MNU-induced retinal degeneration. Furthermore, Msx1-CreERT2 genetic lineage tracing revealed that CE cells migrated into the retina following stimulation and/or injury, where they expressed markers of mature photoreceptors and retinal ganglion cells. Conclusions Together, these results indicate that endogenous adult mammalian RSCs may have latent regenerative potential that can be activated by modulating the RSC niche and hold promise as a means for endogenous retinal cell therapy to repair the retina and improve vision.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
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    Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω 〉 1) had a higher correlation coefficient than that of experienced purifying selection (ω 
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Tectonic inheritance during plate boundary evolution in southern California constrained from seismic anisotropy (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-30
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Geophysical Union
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  • 89
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    Determining the Effect of Varying Magmatic Volatile Content on Lunar Magma Ascent Dynamics (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Print ISSN: 2169-9097
    Electronic ISSN: 2169-9100
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Population Vulnerability to the SARS‐CoV‐2 Virus Infection. A County‐Level Geographical‐Methodological Approach in Romania (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-30
    Electronic ISSN: 2471-1403
    Topics: Geosciences , Medicine
    Published by American Geophysical Union
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    Predicting CMEs using ELEvoHI with STEREO‐HI beacon data (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Print ISSN: 1542-7390
    Electronic ISSN: 1542-7390
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    A practical biphasic contrast media injection protocol strongly enhances the aorta and pulmonary artery simultaneously using a single CT angiography scan (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Enhancement profiles of the pulmonary artery (PA) and aorta differ when using computed tomography (CT) angiography. Our aim was to determine the optimal CT protocol for a one-time CT scan that assesses both blood vessels. Methods We prospectively enrolled 101 cases of CT angiography in patients with suspected pulmonary embolism or aortic dissection from our center between 2018 and 2020. We also retrospectively collected the data of 40 patients who underwent traditional two-time CT scans between 2015 and 2018. Patients were divided into four groups: test bolus (TB) I, TB II, bolus-tracking (BT) I, and BT II. The enhancement of the PA and aorta, and the radiation doses used in the four groups were collected. Those who underwent two-time scans were classified into the traditional PA or aorta scan groups. Data were compared between the BT and traditional groups. Results The aortic enhancement was highest in BT II (294.78 ± 64.48 HU) followed BT I (285.18 ± 64.99 HU), TB II (186.58 ± 57.53 HU), and TB I (173.62 ± 69.70 HU). The radiation dose used was lowest in BT I (11.85 ± 5.55 mSv) and BT II (9.07 ± 3.44 mSv) compared with that used in the traditional groups (20.07 ± 7.78 mSv) and accounted for half of the traditional group (45.17–59.02%). The aortic enhancement was also highest in BT II (294.78 ± 64.48 HU) followed by BT I (285.18 ± 64.99 HU) when compared with that in the traditional aorta scan group (234.95 ± 94.18 HU). Conclusion Our CT protocol with a BT technique allows for a lower radiation dose and better image quality of the PA and aorta than those obtained using traditional CT scans. Trial registration: NCT04832633, retrospectively registered in April 2021 to the clinical trial registry.
    Electronic ISSN: 1471-2342
    Topics: Biology
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    Distinct patterns of whole blood transcriptional responses are induced in mice following immunisation with adenoviral and poxviral vector vaccines encoding the same antigen (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Viral vectors, including adenovirus (Ad) and modified vaccinia Ankara (MVA), have gained increasing attention as vaccine platforms in recent years due to their capacity to express antigens from a wide array of pathogens, their rapid induction of humoral and cellular protective immune responses, and their relatively low production costs. In particular, the chimpanzee Ad vector, ChAdOx1, has taken centre stage as a leading COVID-19 vaccine candidate. However, despite mounting data, both clinical and pre-clinical, demonstrating effective induction of adaptive immune responses, the innate immune signals that precede the protective responses that make these vectors attractive vaccine platforms remain poorly understood. Results In this study, a mouse immunisation model was used to evaluate whole blood gene expression changes 24 h after either a single dose or heterologous prime-boost regimen of an Ad and/or MVA vaccine. We demonstrate through comparative analysis of Ad vectors encoding different antigens that a transgene product-specific gene signature can be discerned from the vector-induced transcriptional response. Expression of genes involved in TLR2 stimulation and γδ T cell and natural killer cell activation were induced after a single dose of Ad, while MVA led to greater expression of type I interferon genes. The order of prime-boost combinations was found to influence the magnitude of the gene expression changes, with MVA/Ad eliciting greater transcriptional perturbation than Ad/MVA. Contrasting the two regimens revealed significant enrichment of epigenetic regulation pathways and augmented expression of MHC class I and II molecules associated with MVA/Ad. Conclusion These data demonstrate that the order in which vaccines from heterologous prime-boost regimens are administered leads to distinct transcriptional responses and may shape the immune response induced by such combinations. The characterisation of early vaccine-induce responses strengthens our understanding of viral vector vaccine mechanisms of action ahead of their characterisation in human clinical trials and are a valuable resource to inform the pre-clinical design of appropriate vaccine constructs for emerging infectious diseases.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to assess potential changes in splicing events in the longissimus dorsi muscle of beef calves gestated under control or methionine-rich diets. RNA sequencing and whole-genome bisulfite sequencing were used to evaluate muscle transcriptome and methylome, respectively. Results Alternative splicing patterns were significantly altered by maternal methionine supplementation. Most of the altered genes were directly implicated in muscle development, muscle physiology, ATP activities, RNA splicing and DNA methylation, among other functions. Interestingly, there was a significant association between DNA methylation and differential exon usage. Indeed, among the set of genes that showed differential exon usage, significant differences in methylation level were detected between significant and non-significant exons, and between contiguous and non-contiguous introns to significant exons. Conclusions Overall, our findings provide evidence that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Slower long‐term coastal warming drives dampened trends in coastal marine heatwave exposure (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Print ISSN: 2169-9275
    Electronic ISSN: 2169-9291
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Abatacept is useful in auto-immune cytopenia with immunopathologic manifestations caused by CTLA-4 defects (2021)
    American Society of Hematology
    Details
    Publication Date: 2021-10-29
    Print ISSN: 0006-4971
    Electronic ISSN: 1528-0020
    Topics: Biology , Medicine
    Published by American Society of Hematology
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    Fortnightly variation of the Tsushima Warm Current on the continental shelf in the southwestern Japan Sea (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Print ISSN: 2169-9275
    Electronic ISSN: 2169-9291
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Phylogenetic profiling is widely used to predict novel members of large protein complexes and biological pathways. Although methods combined with phylogenetic trees have significantly improved prediction accuracy, computational efficiency is still an issue that limits its genome-wise application. Results Here we introduce a new tree-based phylogenetic profiling algorithm named GFICLEE, which infers common single and continuous loss (SCL) events in the evolutionary patterns. We validated our algorithm with human pathways from three databases and compared the computational efficiency with current tree-based with 10 different scales genome dataset. Our algorithm has a better predictive performance with high computational efficiency. Conclusions The GFICLEE is a new method to infers genome-wide gene function. The accuracy and computational efficiency of GFICLEE make it possible to explore gene functions at the genome-wide level on a personal computer.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Polar Mesosphere Summer Echoes and Possible Signatures of Pulsating Aurora Detected by the Meteor Radar (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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    Observations of unusual daytime range spread F at middle latitude during the afternoon hours (2021)
    American Geophysical Union
    Details
    Publication Date: 2021-10-29
    Print ISSN: 1542-7390
    Electronic ISSN: 1542-7390
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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