pinecone/core-2020-05-10-deduplication huggingface dataset:
Decaying lava extrusion rate at El Reventador Volcano, Ecuador measured using high-resolution satellite radar

Lava extrusion at erupting volcanoes causes rapid changes in topography and morphology on the order of tens or even hundreds of metres. Satellite radar provides a method for measuring changes in topographic height over a given time period to an accuracy of metres, either by measuring the width of radar shadow cast by steep sided features, or by measuring the difference in radar phase between two sensors separated in space. We measure height changes, and hence estimate extruded lava volume flux, at El Reventador, Ecuador between 2011 and 2016, using data from the Radarsat-2 and TanDEM-X satellite missions. We find 39 new lava flows were extruded between 9 February 2012 and 24 August 2016, with a cumulative volume of 44.8M m3 dense rock equivalent and a gradually decreasing eruption rate. The average dense rock rate of lava extrusion during this time is 0.31 ± 0.02 m3s−1, which is similar to the long term average from 1972 to 2016. Apart from a volumetrically small dyke opening event between 9 March and 10 June 2012, lava extrusion at El Reventador is not accompanied by any significant magmatic ground deformation. We use a simple physics-based model to estimate that the volume of the magma reservoir under El Reventador is greater than 3 km3. Our lava extrusion data can be equally well fit by models representing a closed reservoir depressurising during the eruption with no magma recharge, or an open reservoir with a time-constant magma recharge rate of up to 0.35 ± 0.01 m3s−
Assessing the variability in the relationship between the particulate backscattering coefficient and the chlorophyll a concentration from a global Biogeochemical-Argo database

Characterizing phytoplankton distribution and dynamics in the world's open oceans requires in situ observations over a broad range of space and time scales. In addition to temperature/salinity measurements, Biogeochemical-Argo (BGC-Argo) profiling floats are capable of autonomously observing at high frequency bio-optical properties such as the chlorophyll fluorescence, a proxy of the chlorophyll a concentration (Chla), the particulate backscattering coefficient (bbp), a proxy of the stock of particulate organic carbon, and the light available for photosynthesis. We analyzed an unprecedented BGC-Argo database of more than 8,500 multi-variable profiles collected in various oceanic conditions, from subpolar waters to subtropical gyres. Our objective is to refine previously established Chla vs bbp relationships and gain insights into the sources of vertical, seasonal and regional variability in this relationship. Despite some nuances in the relationship considering one or another water column layer or region, a general covariation occurs at a global scale. We distinguish two main contrasted situations: (1) concomitant changes in Chla and bbp that correspond to actual variations in phytoplankton biomass, e.g. in subpolar regimes; (2) a decoupling between the two variables attributed to photoacclimation or changes in the relative abundance of non-algal particles, e.g. in subtropical regimes. The variability in the bbp:Chla ratio in the surface layer appears to be essentially influenced by the type of particles and photoacclimation processes. The dense BGC-Argo database helps identifying the spatial and temporal scales at which this ratio is predominantly driven by one or the other of these two factors
Light Absorption by Suspended Particles in the Red Sea: Effect of Phytoplankton Community Size Structure and Pigment Composition

The light absorption properties of phytoplankton (aph(λ)) and non-algal particles (anap(λ)) associated with phytoplankton pigments were analyzed across the Red Sea, in the upper 200 m depth, between October 2014 and August 2016. The contribution by non-algal particles to the total particulate light absorption (aph(λ)+ anap(λ)) was highly variable (23 ± 17% at 440 nm) and no relationship between anap(440) and chlorophyll a concentration, [TChl a], was observed. Phytoplankton specific phytoplankton absorption coefficients at 440 and 676 nm for a given [TChl a], aph*(440) and aph*(676), were slightly higher than those derived from average relationships for open ocean waters within the surface layer as well as along the water column. Variations in the concentration of photosynthetic and photoprotective pigments were noticeable by changes in phytoplankton community size structure as well as in aph*(λ). This study revealed that a higher proportion of picophytoplankton and an increase in photoprotective pigments (mainly driven by zeaxanthin) tended to be responsible for the higher aph*(λ) values found in the Red Sea as compared to other oligotrophic regions with similar [TChl a]. Understanding this variability across the Red Sea may help improve the accuracy of biogeochemical parameters, such as [TChl a], derived from in situ measurements and ocean color remote sensing at a regional scale
Self-organized kilometer-scale shoreline sand wave generation: sensitivity to model and physical parameters

The instability mechanisms for self-organized kilometer-scale shoreline sand waves have been extensively explored by modeling. However, while the assumed bathymetric perturbation associated with the sand wave controls the feedback between morphology and waves, its effect on the instability onset has not been explored. In addition, no systematic investigation of the effect of the physical parameters has been done yet. Using a linear stability model, we investigate the effect of wave conditions, cross-shore profile, closure depth, and two perturbation shapes (P1: cross-shore bathymetric profile shift, and P2: bed level perturbation linearly decreasing offshore). For a P1 perturbation, no instability occurs below an absolute critical angle ¿c0˜ 40-50°. For a P2 perturbation, there is no absolute critical angle: sand waves can develop also for low-angle waves. In fact, the bathymetric perturbation shape plays a key role in low-angle wave instability: such instability only develops if the curvature of the depth contours offshore the breaking zone is larger than the shoreline one. This can occur for the P2 perturbation but not for P1. The analysis of bathymetric data suggests that both curvature configurations could exist in nature. For both perturbation types, large wave angle, small wave period, and large closure depth strongly favor instability. The cross-shore profile has almost no effect with a P1 perturbation, whereas large surf zone slope and gently sloping shoreface strongly enhance instability under low-angle waves for a P2 perturbation. Finally, predictive statistical models are set up to identify sites prone to exhibit either a critical angle close to ¿c0 or low-angle wave instability.Postprint (author's final draft
Pedotransfer functions in Earth system science: challenges and perspectives

Soil, through its various functions, plays a vital role in the Earth's ecosystems and provides multiple ecosystem services to humanity. Pedotransfer functions (PTFs) are simple to complex knowledge rules that relate available soil information to soil properties and variables that are needed to parameterize soil processes. In this paper, we review the existing PTFs and document the new generation of PTFs developed in the different disciplines of Earth system science. To meet the methodological challenges for a successful application in Earth system modeling, we emphasize that PTF development has to go hand in hand with suitable extrapolation and upscaling techniques such that the PTFs correctly represent the spatial heterogeneity of soils. PTFs should encompass the variability of the estimated soil property or process, in such a way that the estimation of parameters allows for validation and can also confidently provide for extrapolation and upscaling purposes capturing the spatial variation in soils. Most actively pursued recent developments are related to parameterizations of solute transport, heat exchange, soil respiration and organic carbon content, root density and vegetation water uptake. Further challenges are to be addressed in parameterization of soil erosivity and land use change impacts at multiple scales. We argue that a comprehensive set of PTFs can be applied throughout a wide range of disciplines of Earth system science, with emphasis on land surface models. Novel sensing techniques provide a true breakthrough for this, yet further improvements are necessary for methods to deal with uncertainty and to validate applications at global scale
Testing the current paradigm for space weather prediction with heliospheric imagers

Predictions of the arrival of four coronal mass ejections (CMEs) in geospace are produced through use of three CME geometric models combined with CME drag modeling, constraining these models with the available Coronagraph and Heliospheric Imager data. The efficacy of these predications is assessed by comparison with the Space Weather Prediction Center (SWPC) numerical MHD forecasts of these same events. It is found that such a prediction technique cannot outperform the standard SWPC forecast at a statistically meaningful level. We test the Harmonic Mean, Self-Similar Expansion, and Ellipse Evolution geometric models, and find that, for these events at least, the differences between the models are smaller than the observational errors. We present a new method of characterizing CME fronts in the Heliospheric Imager field of view, utilizing the analysis of citizen scientists working with the Solar Stormwatch project, and we demonstrate that this provides a more accurate representation of the CME front than is obtained by experts analyzing elongation time maps for the studied events. Comparison of the CME kinematics estimated independently from the STEREO-A and STEREO-B Heliospheric Imager data reveals inconsistencies that cannot be explained within the observational errors and model assumptions. We argue that these observations imply that the assumptions of the CME geometric models are routinely invalidated and question their utility in a space weather forecasting context. These results argue for the continuing development of more advanced techniques to better exploit the Heliospheric Imager observations for space weather forecasting
Isolation of Mycoplasma genitalium from patients with urogenital infections: first report from the Latin-American region

AbstractIsolation of Mycoplasma genitalium from clinical specimens remains difficult. We describe a modified culture system based on Vero cells grown in medium 199 with 2% foetal bovine serum (FBS). The culture system was evaluated using early passage M. genitalium strains M6271 and M6311 with growth monitoring by quantitative TaqMan PCR. Eleven endocervical swabs and one male urethral swab positive by 16S rRNA and MgPal–3 PCRs were quantified and inoculated into Vero cell suspensions in medium 199 supplemented with 2% FBS and antibiotics. Cultures were incubated for 14 days. Cell passages and growth monitoring by TaqMan PCR were performed until the growth of M. genitalium reached ≥106 geq/mL. Confirmation of the new M. genitalium strains was performed by sequencing a 281 bp fragment of mgpB. The growth of Mycoplasma genitalium strains was recorded for all urogenital swab specimens in the modified cell-culture system. Growth of M. genitalium was obtained within 2 months and yielded 12 M. genitalium strains with all 11 isolates from females of an identical, but unique genotype. To our knowledge, this is the first successful isolation of M. genitalium in the Latin-American region. The use of Vero cell culture in 199 medium with 2% FBS is a method comparable to the Ultroser G culture system for isolation of M. genitalium. Genotyping of clinical samples and isolates should be performed to document the absence of cross-contamination
Clinical features of endemic community-acquired psittacosis

AbstractFollowing a large outbreak of community-acquired psittacosis in 2002 in residents of the Blue Mountains, New South Wales, Australia, we reviewed new cases in this area over a 7-year period from 2003 to 2009. Using the 2010 criteria from the Centers for Disease Control National Notifiable Diseases Surveillance System, 85 patients with possible psittacosis were identified, of which 48 were identified as definite or probable infection. Clinical features of these cases are summarized. In addition to Chlamydia-specific serology, specimens, where available, underwent nucleic acid testing for chlamydial DNA using real-time PCR. Chlamydophila psittaci DNA was detected in samples from 23 patients. Four of 18 specimens were culture positive. This is the first description of endemic psittacosis, and is characterized in this location by community-acquired psittacosis resulting from inadvertent exposure to birds. The disease is likely to be under-diagnosed, and may often be mistaken for gastroenteritis or meningitis given the frequency of non-respiratory symptoms, particularly without a history of contact with birds. Clinical characteristics of endemic and outbreak-associated cases were similar. The nature of exposure, risk factors and reasons for the occurrence of outbreaks of psittacosis require further investigation
Dermabacter hominis: a usually daptomycin-resistant gram-positive organism infrequently isolated from human clinical samples

AbstractDuring a 12-year period, Dermabacter hominis was isolated from 21 clinical samples belonging to 14 patients attending a tertiary hospital in León, Spain. Samples included blood cultures (14), peritoneal dialysis catheter exit sites (three), cutaneous abscesses (two), an infected vascular catheter (one) and a wound swab (one). Identification was made by API CoryneTM V2.0, BiologTM GP2 and 16S rRNA gene amplification. Six febrile patients had positive blood cultures (one, two or three sets) and all of them were treated with teicoplanin (two patients), vancomycin, ampicillin plus gentamicin, amoxicillin/clavulanic acid and ciprofloxacin (one each). An additional patient with a single positive blood culture was not treated, the finding being considered non-significant. In the remaining seven patients the organism was isolated from a single specimen and three of them received antimicrobial treatment (ciprofloxacin, ceftriaxone plus vancomycin and amoxicillin/clavulanic acid). At least ten patients had several underlying diseases and conditions, and no direct mortality was observed in relation to the isolated organism. All isolates were susceptible to vancomycin, rifampin and linezolid. Resistance to other antibiotics varied: erythromycin (100%), clindamycin (78.5%), ciprofloxacin (21.4%) and gentamicin, quinupristin-dalfopristin, benzylpenicillin and imipenem 7.1% each. Thirteen isolates were highly resistant to daptomycin with MICs ranging from 8 to 48 (MIC90 = 32 mg/L); only one was daptomycin-sensitive (MIC = 0.19 mg/L)
Actinobaculum schaalii: identification with MALDI-TOF

AbstractActinobaculum schaalii is an emerging uropathogen. So far, its identification has been performed with 16S rRNA gene sequencing or PCR. The diagnosis has often been delayed due to fastidious growth and identification problems. Eleven clinical isolates of A. schaalii from bloodstream infections that were initially identified with 16S rRNA sequencing analysis were recovered and later identified with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). We present a review of bacteriological data of these patients, an algorithm for fast laboratory work-up and advocate the use of sensitized culture of urine to allow better recovery of A. schaalii in susceptible patients
A case of wound infection caused by Shewanella algae in the south of Iran

AbstractShewanella algae was isolated from the purulent discharge in the navel area of a young male with a history of swimming in the Persian Gulf. A routine laboratory diagnosis procedure, followed by 16S rRNA gene sequence analyses, was used to avoid misidentification with other species of Shewanella. The bacterium was suscetible to ceftazidime, ciprofloxacin, nalidixic acid, nitrophorantion, amikacin, ceftriaxone, cefotaxime, gentamicin and co-trimoxazole but was resistant to amoxicillin, vancomycin, doxycycline, cephalexin, ampicillin, tetracycline, cephalothin and ceftizoxime. The patient successfully recovered after treatment with antibiotics
A severe case of persistent diarrhoea associated with Arcobacter cryaerophilus but attributed to Campylobacter sp. and a review of the clinical incidence of Arcobacter spp

AbstractAlthough rarely, Arcobacter spp. have been associated with diarrhoea and bacteraemia. We report a persistent case in a healthy 26-year-old Spanish male of bloody diarrhoea, which was attributed to Campylobacter but in fact was caused by Arcobacter cryaerophilus, as determined by sequencing of the rpoB gene. The isolate was re-identified by matrix-assisted laser desorption ionization time of flight (MALDI-TOF) and genotyped for five putative virulence genes and for seven genes included in the Arcobacter multilocus sequence typing database. The low score obtained by MALDI-TOF indicates the need to complement the database with more isolates. Only the ciaB gene, which encodes for an invasin, was detected. Despite the isolate belonging to a new sequence type, three of the alleles (glnA, pgm and tkt) had been found previously in isolates from faeces of patients with diarrhoea. This study, together with the reviewed literature, indicates that Arcobacter can produce bacteraemia and that the isolation from patients with diarrhoea range from 0.11% to 1.25%. This study also demonstrates that Arcobacter species are confused with Campylobacter spp., as previously suggested. This is one of the factors that leads to underestimation of their incidence together with the use of inappropriate detection and identification methods
Q fever outbreak in the terraced vineyards of Lavaux, Switzerland

Coxiella burnetii infection (Q fever) is a widespread zoonosis with low endemicity in Switzerland, therefore no mandatory public report was required. A cluster of initially ten human cases of acute Q fever infections characterized by prolonged fever, asthenia and mild hepatitis occurred in 2012 in the terraced vineyard of Lavaux. Epidemiological investigations based on patients' interviews and veterinary investigations included environmental sampling as well as Coxiella-specific serological assay and molecular examinations (real-time PCR in vaginal secretions) of suspected sheep. These investigations demonstrated that 43% of sheep carried the bacteria whereas 30% exhibited anti-Coxiella antibodies. Mitigation measures, including limiting human contacts with the flock, hygiene measures, flock vaccination and a public official alert, have permitted the detection of four additional human cases and the avoidance of a much larger outbreak. Since November 2012, mandatory reporting of Q fever to Swiss public health authorities has been reintroduced. A close follow up of human cases will be necessary to identify chronic Q fever
Rothia prosthetic knee joint infection: report and mini-review

AbstractRothia spp. are gram-positive pleomorphic bacteria that are part of the normal oral microflora. They are associated with dental and periodontal disease, although systemic infections have also been reported. We describe the case of a 75-year-old lady with rheumatoid arthritis who presented with prosthetic knee joint infection due to Rothia aeria. We discuss its identification and the evidence regarding association of dental disease with Rothia spp. joint infections based on available literature
Social epigenetics: a science of social science?

The file associated with this record is under a 12-month embargo from publication in accordance with the publisher's self-archiving policy. The full text may be available through the publisher links provided above.Epigenetics has considerable potential to transform social science by embedding mutually regulative reciprocal connections between biological and social processes within the human activities it studies. This paper highlights common epigenetic methods and outlines practical considerations in the design of ‘social epigenetics’ research addressing the identification of biomolecular pathways, statistical inference of causality, conceptualization of the environment as a biochemical event, heritability of epigenetic alterations and intergenerational accountability, and concept of time implied by attempts to capture complex, non-linear gene-environment interactions. Finally, we reflect on the social epigenome as a conceptual space and try to identify barriers to translation, and practical and ethical issues raised by epigenetics research. In order for social epigenetics and social science to contribute to the emergence of this putative ‘science of social science’ and to capture meaningful human experience they will both need to change significantly.Peer-reviewedPost-prin
A comparative proteomics study of a synovial cell line stimulated with TNF-α

To elucidate the pathogenesis of rheumatoid arthritis (RA), we used proteomic analysis to determine the protein profile in a synovial cell line, MH7A, established from patients with RA. Proteins were extracted from MH7A cells that were or were not stimulated with tumor necrosis factor-α (TNF-α), and then analyzed on a liquid chromatography/mass spectrometry system equipped with a unique long monolithic silica capillary. On the basis of the results of this proteomic analysis, we identified 2650 proteins from untreated MH7A cells and 2688 proteins from MH7A cells stimulated with TNF-α. Next, we selected 269 differentially produced proteins that were detected only under TNF-α stimulation, and classified these proteins by performing gene ontology analysis by using DAVID as a functional annotation tool. In TNF-α-stimulated MH7A cells, we observed substantial production of plasminogen-activator inhibitor 2 and apoptosis-regulating proteins such as BH3-interacting domain death agonist, autophagy protein 5, apolipoprotein E, and caspase-3. These results indicate that the upregulation of plasminogen-activator inhibitor 2 and apoptosis-regulating proteins in synovial cells in response to TNF-α stimulation might represent a predominant factor that contributes to the pathogenesis of RA
MafB deficiency accelerates the development of obesity in mice

MafB, a transcription factor expressed selectively in macrophages, has important roles in some macrophage-related diseases, especially in atherosclerosis. In this study, we investigated the mechanism by which hematopoietic-specific MafB deficiency induces the development of obesity. Wild-type and hematopoietic cell-specific Mafb-deficient mice were fed a high-fat diet for 10 weeks. The Mafb-deficient mice exhibited higher body weights and faster rates of body weight increase than control mice. The Mafb-deficient mice also had a higher percentage of body fat than the wild-type mice, due to increased adipocyte size and serum cholesterol levels. Reverse transcription-PCR analysis showed a reduction in apoptosis inhibitor of macrophage (AIM) in Mafb-deficient adipose tissue. AIM is known as an inhibitor of lipogenesis in adipocytes and is expressed in adipose tissue macrophages. Collectively, our data suggest that Mafb deficiency in hematopoietic cells accelerates the development of obesity