bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Magnetic Storm Related Thermospheric Changes on the Evolution of Equatorial Plasma Bubbles
Authors: Bhattacharyya A. , Fedrizzi M. , Fuller‐Rowell T. J. , Gurram P. , Kakad B. , Sripathi S. , Sunda S. 
Published: February 2019

AbstractPast efforts to predict scintillations on VHF and L‐band radio signals recorded at equatorial and low‐latitude stations have been mostly based on a theoretical linear growth rate of Rayleigh‐Taylor instability on the bottomside of the post‐sunset equatorial F layer, which is responsible for the generation of an equatorial plasma bubble (EPB). However, it is the maximum height that an EPB reaches above the dip equator and development of intermediate scale irregularities within the EPB, in its nonlinear phase of evolution that determines the latitudinal distribution of scintillations. Amplitude scintillations recorded by a network of VHF and L‐band receivers on a quiet day, 13 March 2015 and on 20 March 2015, a few days after the 17 March 2015 magnetic storm, show that latitudinal extent of scintillations caused by EPB irregularities is lesser on 20 March than on 13 March. Geomagnetic and ionosonde data from an equatorial station, and vertical total electron content distributions obtained from Global Navigation Satellite Systems observations, indicate that the equatorial ionospheric conditions are approximately same on these 2 days. Simulation of thermospheric conditions for these 2 days is carried out using the Coupled Thermosphere, Ionosphere, Plasmasphere, and Electrodynamics model. It is found that thermospheric atomic oxygen density is enhanced in the aftermath of the major magnetic storm of 17 March 2015, resulting in enhanced ion‐neutral collision frequencies over the dip equator on 20 March. This limits the height to which an EPB rises over the dip equator on this day, and thus impacts the latitudinal distribution of scintillations.
A Solar Signature in Many Climate Indices
Authors: Le Mouël Jean‐Louis , Lopes Fernand , Courtillot Vincent 
Published: February 2019

AbstractWe first apply singular spectrum analysis (SSA) to the international sunspot number (1849–2015) and the count of polar faculae (1906–2006). The SSA method finds 22‐, 11‐, and 5.5‐year components as the first eigenvectors of these solar activity proxies. We next apply SSA to the 10 Madden‐Julian oscillation (MJO; 1978–2016) indices. The first, most intense component SSA finds in all MJO indices has either a period of 5.5 or 11 years. The longer‐term modulation of amplitude is on the order of one third of the total variation. The 5.5‐year SSA component 1 of most MJO indices moreover follows the decreasing amplitude of solar cycles. We then apply SSA to climate indices Pacific Decadal Oscillation, El Nino Southern Oscillation precipitation index, Arctic Oscillation, Atlantic Multidecadal oscillation, Tropical Southern Atlantic oscillation, Western Hemisphere Warm Pool, and Brazil and Sahel rainfalls. We find that the first SSA eigenvectors are all combinations of rather pure 11, 5.5, and 3.6‐year pseudo‐cycles. The 5.5‐year component is frequently observed and is particularly important and sharp in the series in which it appears. All these periods have long been attributed to solar activity, and this by itself argues for the existence of a strong link between solar activity and climate. The mechanisms of coupling must be complex and probably nonlinear but they remain to be fully understood (UV radiation, solar wind, and galactic cosmic rays being the most promising candidates). We propose as a first step a Kuramoto model of nonlinear coupling that generates phase variations compatible with the observed ones.
Estimation of Average Diffuse Aquifer Recharge Using Time Series Modeling of Groundwater Heads
Authors: Obergfell Christophe , Bakker Mark , Maas Kees 
Published: February 2019

AbstractA new method is presented to estimate average diffuse aquifer recharge of water table aquifers in temperate climates using time series analysis of water table level fluctuations. An accurate estimate of the recharge caused by rainfall requires an accurate estimate of the influence of evaporation. In temperate climates, evaporation imprints a seasonal component in the water table fluctuations. As such, recharge is estimated from time series models fitted to observed heads under the additional constraint that the seasonal harmonic of the observed head is reproduced as the sum of the transformed seasonal harmonics present in precipitation, evaporation, and pumping. An explicit equation is presented, in terms of the model parameters, for the damping and phase shift of the response to the seasonal harmonic of the stresses. Taking into account the seasonal harmonic of the observed heads results in more reliable recharge estimates compared to standard time series analysis. The method is limited to systems that are sufficiently linear and that remain unaltered over the analysis period. Head fluctuations and stresses should contain a seasonal harmonic that can be estimated with accurately. Runoff must be negligible or quantifiable. The method is applied to measured heads obtained from piezometers situated on and around the ice‐pushed sand ridge of Salland in the Netherlands and compares well with recharge estimates based on the saturated zone chloride mass balance.
Comparison of visceral fat measurement by dual-energy X-ray absorptiometry to computed tomography in HIV and non-HIV
Authors: Fourman Lindsay T. , Kileel Emma M. , Hubbard Jane , Holmes Tara , Anderson Ellen J. , Looby Sara E. , Fitch Kathleen V. , Feldpausch Meghan N. , Torriani Martin , Lo Janet , Stanley Takara L. , Grinspoon Steven K. 
Published: February 2019

Abstract
Background/Objectives
Individuals with HIV are susceptible to visceral fat accumulation, which confers an increased risk of cardiometabolic disease. Advanced software to ascertain visceral fat content from dual-energy X-ray absorptiometry (DXA) has not been validated among this population. We sought to compare DXA with computed tomography (CT) in the measurement of visceral fat cross-sectional area (VAT) in HIV and non-HIV using Bland–Altman analyses.

Subjects/Methods
Data were combined from five previously conducted studies of individuals with HIV (n = 313) and controls without HIV (n = 144) in which paired DXA and CT scans were available. In cross-sectional analyses, DXA-VAT was compared with CT-VAT among participants with and without HIV. In longitudinal analyses, changes in VAT over time were compared between DXA and CT among participants with and without HIV receiving no intervention over 12 months and among individuals with HIV receiving tesamorelin—a medication known to reduce VAT—over 6 months.

Results
In HIV, DXA underestimated VAT compared with CT among individuals with increased visceral adiposity. The measurement bias was −9 ± 47 cm2 overall, but became progressively larger with greater VAT (P < 0.0001), e.g., −61 ± 58 cm2 among those with VAT ≥ 200 cm2. Sex-stratified analyses revealed that the relationship between VAT and measurement bias was especially pronounced in men (P < 0.0001). Longitudinally, DXA underestimated changes in VAT, particularly among those at the extremes of VAT gain or loss (P < 0.0001). In contrast to the cross-sectional findings, the tendency for DXA to underestimate longitudinal changes in VAT was evident in both men and women. Analogous findings were seen among controls in cross-sectional and longitudinal analyses.

Conclusions
DXA underestimated VAT relative to CT in men with and without HIV, who had increased visceral adiposity. DXA also underestimated changes in VAT over time in men and women, irrespective of HIV status. DXA-VAT should be used with caution among both HIV and non-HIV-infected populations.
The prediction of suicide in severe mental illness: development and validation of a clinical prediction rule (OxMIS)
Authors: Fazel Seena , Wolf Achim , Larsson Henrik , Mallett Susan , Fanshawe Thomas R. 
Published: February 2019

AbstractAssessment of suicide risk in individuals with severe mental illness is currently inconsistent, and based on clinical decision-making with or without tools developed for other purposes. We aimed to develop and validate a predictive model for suicide using data from linked population-based registers in individuals with severe mental illness. A national cohort of 75,158 Swedish individuals aged 15–65 with a diagnosis of severe mental illness (schizophrenia-spectrum disorders, and bipolar disorder) with 574,018 clinical patient episodes between 2001 and 2008, split into development (58,771 patients, 494 suicides) and external validation (16,387 patients, 139 suicides) samples. A multivariable derivation model was developed to determine the strength of pre-specified routinely collected socio-demographic and clinical risk factors, and then tested in external validation. We measured discrimination and calibration for prediction of suicide at 1 year using specified risk cut-offs. A 17-item clinical risk prediction model for suicide was developed and showed moderately good measures of discrimination (c-index 0.71) and calibration. For risk of suicide at 1 year, using a pre-specified 1% cut-off, sensitivity was 55% (95% confidence interval [CI] 47–63%) and specificity was 75% (95% CI 74–75%). Positive and negative predictive values were 2% and 99%, respectively. The model was used to generate a simple freely available web-based probability-based risk calculator (Oxford Mental Illness and Suicide tool or OxMIS) without categorical cut-offs. A scalable prediction score for suicide in individuals with severe mental illness is feasible. If validated in other samples and linked to effective interventions, using a probability score may assist clinical decision-making.
CXCR7 promotes melanoma tumorigenesis via Src kinase signaling
Authors: Xu Siran , Tang Jiaze , Wang Chunying , Liu Jie , Fu Yan , Luo Yongzhang 
Published: February 2019

AbstractChemokine receptors have been documented to exert critical functions in melanoma progression. However, current drugs targeting these receptors have limited efficacy in clinical applications, suggesting the urgency to further explore the roles of chemokine receptors in melanoma. Here we found that C–X–C chemokine receptor 7 (CXCR7) was the most highly expressed chemokine receptor in murine melanoma cell lines. In addition, the expression level of CXCR7 was positively correlated with melanoma progression in the clinical samples. High CXCR7 expression was associated with shorter overall survival in melanoma patients. Increased expression of CXCR7 augmented melanoma proliferation in vitro and tumor growth in vivo, whereas knockout of CXCR7 exhibited significant inhibitory effects. Moreover, our data elucidated that CXCR7 activated Src kinase phosphorylation in a β-arrestin2-dependent manner. The administration of the Src kinase inhibitor PP1 or siRNA specific for β-arrestin2 abolished CXCR7-promoted cell proliferation. Importantly, CXCR7 also regulated melanoma angiogenesis and the secretion of vascular endothelial growth factor (VEGF). Subsequent investigations revealed a novel event that the activation of the CXCR7-Src axis stimulated the phosphorylation of eukaryotic translation initiation factor 4E (eIF4E) to accelerate the translation of hypoxia-inducible factor 1α (HIF-1α), which enhanced the secretion of VEGF from melanoma cells. Collectively, our results illuminate the crucial roles of CXCR7 in melanoma tumorigenesis, and indicate the potential of targeting CXCR7 as new therapeutic strategies for melanoma treatment.
Surface tension and viscosity of liquid Pd43Cu27Ni10P20 measured in a levitation device under microgravity
Authors: Mohr Markus , Wunderlich Rainer K. , Zweiacker Kai , Prades-Rödel Silke , Sauget Romuald , Blatter Andreas , Logé Roland , Dommann Alex , Neels Antonia , Johnson William L. , Fecht Hans-Jörg 
Published: February 2019

AbstractHere we present measurements of surface tension and viscosity of the bulk glass-forming alloy Pd43Cu27Ni10P20 performed during containerless processing under reduced gravity. We applied the oscillating drop method in an electromagnetic levitation facility on board of parabolic flights. The measured viscosity exhibits a pronounced temperature dependence following an Arrhenius law over a temperature range from 1100 K to 1450 K. Together with literature values of viscosity at lower temperatures, the viscosity of Pd43Cu27Ni10P20 can be well described by a free volume model. X-ray diffraction analysis on the material retrieved after the parabolic flights confirm the glassy nature after vitrification of the bulk samples and thus the absence of crystallization during processing over a wide temperature range.
Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes
Authors: Regan-Fendt Kelly E. , Xu Jielin , DiVincenzo Mallory , Duggan Megan C. , Shakya Reena , Na Ryejung , Carson William E. , Payne Philip R. O. , Li Fuhai 
Published: February 2019

AbstractSystems biology perspectives are crucial for understanding the pathophysiology of complex diseases, and therefore hold great promise for the discovery of novel treatment strategies. Drug combinations have been shown to improve durability and reduce resistance to available first-line therapies in a variety of cancers; however, traditional drug discovery approaches are prohibitively cost and labor-intensive to evaluate large-scale matrices of potential drug combinations. Computational methods are needed to efficiently model complex interactions of drug target pathways and identify mechanisms underlying drug combination synergy. In this study, we employ a computational approach, SynGeNet (Synergy from Gene expression and Network mining), which integrates transcriptomics-based connectivity mapping and network centrality analysis to analyze disease networks and predict drug combinations. As an exemplar of a disease in which combination therapies demonstrate efficacy in genomic-specific contexts, we investigate malignant melanoma. We employed SynGeNet to generate drug combination predictions for each of the four major genomic subtypes of melanoma (BRAF, NRAS, NF1, and triple wild type) using publicly available gene expression and mutation data. We validated synergistic drug combinations predicted by our method across all genomic subtypes using results from a high-throughput drug screening study across. Finally, we prospectively validated the drug combination for BRAF-mutant melanoma that was top ranked by our approach, vemurafenib (BRAF inhibitor) + tretinoin (retinoic acid receptor agonist), using both in vitro and in vivo models of BRAF-mutant melanoma and RNA-sequencing analysis of drug-treated melanoma cells to validate the predicted mechanisms. Our approach is applicable to a wide range of disease domains, and, importantly, can model disease-relevant protein subnetworks in precision medicine contexts.
A mycobacterial disease is associated with the silent mass mortality of the pen shell Pinna nobilis along the Tyrrhenian coastline of Italy
Authors: Carella F. , Aceto S. , Pollaro F. , Miccio A. , Iaria C. , Carrasco N. , Prado P. , De Vico G. 
Published: February 2019

AbstractDisease is an increasing threat for marine bivalves worldwide. Recently, a mass mortality event (MME) impacting the bivalve Pinna nobilis was detected across a wide geographical area of the Spanish Mediterranean Sea and linked to a haplosporidian parasite. In 2017–2018, mass mortality events affecting the pen shell Pinna nobilis were recorded in two different regions of Italy, Campania and Sicily, in the Tyrrhenian Sea (Mediterranean Sea). Histopathological and molecular examinations of specimens showed the presence of Haplosporidium sp. in only one specimen in one area. Conversely, in all of the surveyed moribund animals, strong inflammatory lesions at the level of connective tissue surrounding the digestive system and gonads and linked to the presence of intracellular Zhiel-Neelsen-positive bacteria were observed. Molecular analysis of all of the diseased specimens (13) confirmed the presence of a Mycobacterium. Blast analysis of the sequences from all of the areas revealed that they were grouped together with the human mycobacterium M. sherrisii close to the group including M. shigaense, M. lentiflavum and M. simiae. Based on pathological and molecular findings, it is proposed that a mycobacterial disease is associated with the mortality episodes of Pinna nobilis, indicating that, at this time, Haplosporidium sp. is not responsible for these events in Campanian and Sicilian waters.
Low temperature-induced variation in plasma biochemical indices and aquaglyceroporin gene expression in the large yellow croaker Larimichthys crocea
Authors: Liu Cheng , Shen Weiliang , Hou Congcong , Gao Xinming , Wang Qianfeng , Wu Xiongfei , Zhu Junquan 
Published: February 2019

AbstractLow temperature influences multiple physiological processes in fish. To explore the adaptability of the large yellow croaker (Larimichthys crocea) to low temperature, the concentrations of glycerol, blood urea nitrogen (BUN), and triglycerides (TG) in plasma, as well as the expression levels of metabolism-related genes aqp7 and aqp10, were measured after exposure to low temperature stress and during subsequent rewarming. In addition, tissue samples from the intestine and liver were histologically analyzed. We found that the concentrations of plasma glycerol, BUN, and TG, decreased under low temperature stress, suggesting the metabolism of fat and protein slowed at low temperature. The expression levels of aqp7 and aqp10 mRNA were also downregulated under exposure to low temperature. Interestingly, above plasma indices and gene expression returned to basic levels within 24 h after rewarming. Furthermore, the liver and the intestine were damaged under continuous low temperature stress, whereas they were repaired upon rewarming. From the above results, we concluded that aqp7 and aqp10 genes were sensitive to low temperature, and that the decrease in their expression levels at low temperature might reduce energy consumption by L. crocea. However, the adaptation to low temperature was limited because the key metabolic tissues were damaged under continuous exposure to low temperature. Interestingly, the metabolism of L. crocea was basically back to normal within 24 h of rewarming, showing that it has high capacity of self-recovery.
Effect of Lure Combination on Fruit Fly Surveillance Sensitivity
Authors: Stringer Lloyd D. , Soopaya Rajendra , Butler Ruth C. , Vargas Roger I. , Souder Steven K. , Jessup Andrew J. , Woods Bill , Cook Peter J. , Suckling David Maxwell 
Published: February 2019

AbstractSurveillance for invading insect pests is costly and the trapper usually finds the traps empty of the target pest. Since the successful establishment of new pests is an uncommon event, multiple lures placed into one trap might increase the efficiency of the surveillance system. We investigated the effect of the combination of the Tephritidae male lures – trimedlure, cuelure, raspberry ketone and methyl eugenol – on catch of Ceratitis capitata, Zeugodacus cucurbitae, Bactrocera tryoni, B. dorsalis, B. aquilonis and B. tenuifascia in Australia and the USA (not all species are present in each country). The increase in trap density required to offset any reduction in catch due to the presence of lures for other Tephritidae was estimated. The effect of increasing trap density to maintain surveillance sensitivity was modelled for a hypothetical population of B. tryoni males, where the effective sampling area of cuelure traps for this species has been estimated. The 3-way combination significantly reduced the catch of the methyl eugenol-responsive B. dorsalis. Unexpectedly, we found that trimedlure-baited traps that contained methyl eugenol had ×3.1 lower catch of C. capitata than in trimedlure-only-baited traps in Australia, but not in Hawaii where no difference in catch was observed, we cannot satisfactorily explain this result. Based on the data presented here and from previous research, combinations of some male lures for the early detection of tephritid flies appear compatible and where there is any reduction in surveillance sensitivity observed, this can be offset by increasing the density of traps in the area.
An Archaeometric Characterization of Ecuadorian Pottery
Authors: Sánchez-Polo Alejandra , Briceño Sarah , Jamett Alex , Galeas Salomé , Campaña Orlando , Guerrero Víctor , Arroyo Carlos R. , Debut Alexis , Mowbray Duncan J. , Zamora-Ledezma Camilo , Serrano Jorge 
Published: February 2019

AbstractEcuadorian pottery is renowned for its beauty and the particularly rich colour of its pigments. However, a major challenge for art historians is the proper assessment of the provenance of individual pieces due to their lack of archaeological context. Of particular interest is the Jama-Coaque culture, which produced fascinating anthropomorphic and zoomorphic pottery from ca. 240 B.C. until the Spanish Conquest of 1532 A.D. in the coastal region of Ecuador. Using a combination of microscopic and spectroscopic techniques, i.e., transmission electron microscopy (TEM), Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), energy-dispersive x-ray spectroscopy (EDX), and scanning electron microscopy (SEM); we are able to characterize these pieces. We have found several kinds of iron-oxide based nanostructures in all the colour pigments we investigated for the Jama-Coaque culture, suggesting the same unique volcanic source material was used for their clay. Such nanostructures were absent from the pigment samples studied from other contemporary coastal-Ecuadorian cultures, i.e., the Tumaco-La Tolita and Bahía cultures. In the yellow pigments of goethite we find carbon nanofibres, indicating these pigments were subjected to a thermal treatment. Finally, in the blue, green, and black pigments we detect modern pigments (phthalocyanine blue, lithopone, and titanium white), suggesting modern restoration. Our results demonstrate the power of TEM, Raman, FTIR, EDX, and SEM archaeometric techniques for characterizing pieces without a clear archaeological context. Furthermore, the characterization of nanostructures present in such pieces could be used as a possible fingerprint for a provenance study.
The bacterial community of Quesnel Lake sediments impacted by a catastrophic mine tailings spill differ in composition from those at undisturbed locations – two years post-spill
Authors: Hatam I. , Petticrew E. L. , French T. D. , Owens P. N. , Laval B. , Baldwin S. A. 
Published: February 2019

AbstractThe West Basin of Quesnel Lake (British Columbia, Canada) suffered a catastrophic disturbance event in August 2014 when mine tailings and scoured natural material were deposited into the lake’s West Basin due to an impoundment failure at the adjacent Mount Polley copper-gold mine. The deposit covered a significant portion of the West Basin floor with a thick layer of material. Since lake sediments host bacterial communities that play key roles in the geochemical cycling in lacustrine environments, it is important to understand which groups inhabit the newly deposited material and what this implies for the ecological function of the West Basin. Here we report a study conducted two years post-spill, comparing the bacterial communities from sediments of both disturbed and undisturbed sites. Our results show that sediments from disturbed sites differed in physical and chemical properties than those in undisturbed sites (e.g. higher pH, particle size and Cu concentration). Furthermore, bacterial communities from the disturbed sites appeared to be legacy communities from the tailings impoundment, with metabolic potential revolving mainly around the cycling of S and metals, whereas the ones from the undisturbed sites were associated with the cycling of N.