bluuebunny/crossref_metadata_2025 huggingface dataset:
Urinary Excretion of Anthocyanins Following Consumption of Strawberry and Red Grape Juice
Authors: Cahyana Yana , Gordon Michael H. , Gibson Trevor M.
Published: February 2019

Abstract. The excretion of anthocyanins in urine following consumption of a mixed juice prepared from strawberry and red grape juice was investigated in a human intervention study. Unmetabolised anthocyanins, and glucuronide derivatives have been detected, with pelargonidin-3 glucoside metabolised into pelargonidin monoglucuronide and pelargonidin-3-glucoside monoglucuronide. The mass of urinary anthocyanins excreted in 24 h following consumption of the mixed juice (containing 21.93 mg of anthocyanins) was 144 nmol consisting of 106 nmol of anthocyanins derived from strawberries (0.32% of ingested dose) and 38 nmol derived from red grapes (0.22% of ingested dose). A higher proportion of delphinidin–3-glucoside was excreted in the unmetabolised form than less polar anthocyanins (at p ≤ 0.05). Excretion of anthocyanins peaked between 2 and 4 h following consumption of the juice. The proportion of the ingested anthocyanins excreted was not significantly different for strawberry and red grape anthocyanins despite the differences in the structures.
Reef‐Scale‐Dependent Response of Massive Porites Corals From the Central Indian Ocean to Prolonged Thermal Stress: Evidence From Coral Sr/Ca Measurements
Authors: Leupold Maike , Pfeiffer Miriam , Garbe‐Schönberg Dieter , Sheppard Charles
Published: February 2019

Here we present coral Sr/Ca data of biweekly resolution from three modern coral cores drilled from living Porites corals from two different reef settings at Chagos (tropical Indian Ocean). Chagos lies at the eastern margin of the Seychelles‐Chagos thermocline ridge and features open ocean upwelling. In situ temperatures have been recorded by temperature loggers since 2006. High‐resolution satellite temperatures closely track the logger data. Two cores were collected from a patch reef in the lagoon of Peros Banhos, a site characterized by high mean temperatures and low‐temperature variability. An open ocean core was collected at the outer reef slope of Diego Garcia, which experiences larger temperature fluctuations related to open ocean upwelling. The open ocean core shows clear seasonal cycles in Sr/Ca that closely track the satellite temperatures. The Sr/Ca records from the two lagoon corals show good reproducibility. Between 2007 and 2010, Sr/Ca tracks satellite temperatures. However, between 2003 and 2006 the Sr/Ca curves are almost flat and annual coral growth rates are low. During these years, warm sea surface temperatures and coral bleaching have been observed at Chagos. It is likely that the observed reduction in coral growth rates is a response to prolonged warming events, adding to the growing evidence that seemingly healthy and surviving corals are affected by thermal stress. Further, the high correlation between the Sr/Ca records of the two lagoon cores suggests that this effect is not limited to single coral colonies but may affect the entire reef setting.
Striations in Marginal Seas and the Mediterranean Sea
Authors: Zhang Y. , Guan Y. P.
Published: February 2019

Striations, which are jet‐like structures comprising alternating ridges and furrows within large‐scale circulations, are widely studied in the open ocean, although it is unclear whether they exist in marginal or semiclosed seas. Based on an appropriate choice of averaging time scale and cutoff wavelength, our analysis reveals striations in marginal seas, including the South China Sea (SCS), Sea of Japan, and Gulf of Mexico, and in the Mediterranean Sea (MS). Compared with the open ocean, these striations have a narrower bandwidth (about 60 km in marginal seas and 100 km in the MS), fewer zonal orientations, stronger baroclinic structure, and deeper intensification. Striations in the open ocean are usually barotropic; however, within the South China Sea and MS, they are baroclinic in the upper 1,000 m and intensified at depths greater than 3,000 m.
Wind Power on Oceanic Near‐Inertial Oscillations in the Global Ocean Estimated From Surface Drifters
Authors: Liu Yongzheng , Jing Zhao , Wu Lixin
Published: February 2019

Wind power on oceanic near‐inertial oscillations is thought to play an important role in furnishing the diapycnal mixing in the ocean. Yet their global distribution and magnitude have not been quantified based on observations. In this study, we use hourly ocean current records derived from surface drifters to compute the global near‐inertial wind power during 1993–2016, with a combination of surface wind measurements obtained from satellites. The climatological near‐inertial wind power integrated between 60°S and 60°N is estimated to be 0.3–0.6 TW. The strongest energy flux occurs in the 30–60° latitude band during the winter season as a result of energetic storm activities. Ocean current imprint on wind stress has a significant impact on the estimated global near‐inertial wind power from drifters. Neglecting this imprint overestimates the near‐inertial wind power locally by 25–120% and its global mean value by 60%.
Aerosol Indirect Effects in Marine Stratocumulus: The Importance of Explicitly Predicting Cloud Droplet Activation
Authors: Bulatovic I. , Ekman A. M. L. , Savre J. , Riipinen I. , Leck C.
Published: February 2019

Climate models generally simulate a unidirectional, positive liquid water path (LWP) response to increasing aerosol number concentration. However, satellite observations and large‐eddy simulations show that the LWP may either increase or decrease with increasing aerosol concentration, influencing the overall magnitude of the aerosol indirect effect (AIE). We use large‐eddy simulation to investigate the LWP response of a marine stratocumulus cloud and its dependence on different parameterizations for obtaining cloud droplet number concentration (CDNC). The simulations confirm that the LWP response is not always positive—regardless of CDNC treatment. However, the AIE simulated with the model version with prescribed CDNC is almost 3 times larger compared to the version with prognostic CDNC. The reason is that the CDNC in the prognostic scheme varies in time due to supersaturation fluctuations, collection, and other microphysical processes. A substantial spread in simulated AIE may thus arise simply due to the CDNC treatment.
The Extra‐Magnetospheric Ion Environment as Observed by the Magnetospheric Multiscale Mission Hot Plasma Composition Analyzer (MMS‐HPCA)
Authors: Gomez R. G. , Fuselier S. A. , Mukherjee J. , Gonzalez C. A. , Burch J. L. , Strangeway R. J. , Starkey M. J.
Published: February 2019

Observations within the solar wind (SW) environment outside of the Earth's magnetosphere were conducted on 6 December 2016, by the Hot Plasma Composition Analyzer of the Magnetospheric Multiscale mission. At the time of measurement, the SW was in a compressed state with a southbound interplanetary magnetic field of 9 nT and corresponding increases in proton density and dynamic pressure. High time resolution measurements of pickup ions in this region were made during the time when the Earth is situated in a solar gravitational focusing cone for interstellar neutrals. Proton measurements revealed a suprathermal ion population traveling with a maximum velocity that is two and a half times that of the SW velocity (Vsw). Helium ions exhibited pitch angle scattering that was uncorrelated with changes in the interplanetary magnetic field orientation. The time‐of‐flight measurements exhibited expected contributions from both protons and singly charged helium. Because the Magnetospheric Multiscale spacecraft are in the SW, counts from heavy SW ions (possibly Fe7+ or Fe8+) with M/Q = 8 AMU/e are observed with a mean energy/charge (E/Q) of 5.75 keV/e.
The Impact of Rheology on the Transition From Stick‐Slip to Creep in a Semibrittle Analog
Authors: Birren T. , Reber J. E.
Published: February 2019

Faults can release energy via a variety of different slip mechanisms ranging from steady creep to fast and destructive earthquakes. Tying the rheology of the crust to various slip dynamics is important for our understanding of plate tectonics and earthquake generation. Here we propose that the interplay of fractures and viscous flow leads to a spectrum between stick‐slip and creep. We use an elasto‐visco‐plastic rock analog (Carbopol U‐21) where we vary the yield stress to investigate its impact on slip dynamics in shear experiments. The experiments are performed using a simple shear apparatus, which provides distributed shear across the entire width of the experiment and allows in situ observations of deformation. We record force and displacement during deformation and use time lapse photography to document fracture development. A low yield stress (25 Pa) leads to creep dynamics in the absence of fractures. An intermediate yield stress (144 Pa) leads to the development and interaction of opening (mode I) and shear (mode II) fractures. This interaction leads to a spectrum in slip dynamics ranging from creep to stick‐slip. A high yield stress (357 Pa) results in the development of many mode I fractures and a deformation signal dominated by stick‐slip. These results show that bulk yield stress, fracture formation, and slip dynamics are closely linked and can lead to a continuum between creep and stick‐slip. We suggest that rheology should be considered as an additional mechanism to explain the broad range of slip dynamics in natural faults.
The Structure and Entrainment Characteristics of Partially Confined Gravity Currents
Authors: Kelly R. W. , Dorrell R. M. , Burns A. D. , McCaffrey W. D.
Published: February 2019

Seafloor channels are the main conduit for turbidity currents transporting sediment to the deep ocean, and they can extend for thousands of kilometers along the ocean floor. Although it is common for channel‐traversing turbidity currents to spill onto levees and other out‐of‐channel areas, the associated flow development and channel‐current interaction remain poorly understood; much of our knowledge of turbidity current dynamics comes from studies of fully confined scenarios. Here we investigate the role that partial lateral confinement may play in affecting turbidity current dynamics. We report on laboratory experiments of partially confined, dilute saline flows of variable flux rate traversing fixed, straight channels with cross‐sectional profiles representative of morphologies found in the field. Complementary numerical experiments, validated against high‐resolution laboratory velocity data, extend the scope of the analysis. The experiments show that partial confinement exerts a first‐order control on flow structure. Overbank and downstream discharges rapidly adjust over short length scales, providing a mechanism via which currents of varying sizes can be tuned by a channel and conform to a given channel geometry. Across a wide range of flow magnitudes and states of flow equilibration to the channel, a high‐velocity core remains confined within the channel with a constant ratio of velocity maximum height to channel depth. Ongoing overbank flow prevents any flow thickening due to ambient entrainment, allowing stable downstream flow evolution. Despite dynamical differences, the entrainment rates of partially confined and fully confined flows remain comparable for a given Richardson number.
Modeling the Transition to High Sediment Concentrations as a Response to Channel Deepening in the Ems River Estuary
Authors: Dijkstra Yoeri M. , Schuttelaars Henk M. , Schramkowski George P. , Brouwer Ronald L.
Published: February 2019

Many estuaries are strongly modified by human interventions, including substantive channel deepening. In the Ems River Estuary (Germany and Netherlands), channel deepening between the 1960s and early 2000s coincided with an increase in the maximum near‐bed suspended sediment concentration from moderate (∼1 kg/m3) to high (>10 kg/m3). In this study the observed transition in the suspended sediment concentration in the Ems is qualitatively reproduced by using an idealized width‐averaged iFlow model. The model is used to reproduce observations from 1965 and 2005 by only changing the channel depth between the years. Model results show an increase in sediment concentrations from approximately 1–2 kg/m3 to 20–30 kg/m3 near the bed between 1965 and 2005 if the river discharge is below 70 m3/s, which holds approximately 60% of the time. Thereby, this study for the first time provides strong evidence for earlier published hypotheses that channel deepening was the main driver of the increased sediment concentrations in the Ems. The results are explained using two aspects: sediment transport (longitudinal processes) and local resuspension (vertical processes). The magnitude of the sediment import increased, because a combination of channel deepening and sediment‐induced damping of turbulence increased the M2–M4 tidal asymmetry. This effect is particularly strong, because the M4 tide evolved to a state close to resonance. All imported sediment is kept in suspension when it is assumed that resuspension is sufficiently efficient, which depends on the value of the erosion parameter used and inclusion of hindered settling in the model.
Variability of Surface Water pCO2 in the Canadian Arctic Archipelago From 2010 to 2016
Authors: Ahmed M. , Else B. G. T. , Burgers T. M. , Papakyriakou T.
Published: February 2019

This study provides 6 years of high‐resolution underway measurements of the sea surface partial pressure of CO2 (pCO2sw), sea surface temperature, and salinity across the Canadian Arctic Archipelago (CAA). Observed pCO2sw varied regionally, with the northern and central channels of the CAA undersaturated in pCO2sw (with respect to the atmosphere), while the western regions were typically saturated to supersaturated in pCO2sw. This apparent spatial variability was caused to some extent by the timing of our ship transit through the CAA, as we also found a general seasonal trend of pCO2sw being undersaturated in the early summer, followed by saturation to supersaturation in late summer, and a return to undersaturation during the autumn. Sea surface temperature was significantly correlated with pCO2sw at various locations across the CAA, but we also observed the effects of other regional processes like upwelling, primary production, riverine input, and sea ice melt. These processes are linked to each other, and hence, it is impossible to pinpoint only one dominant factor controlling pCO2sw variability in the CAA. However, we found that sea ice dominates the seasonal cycle of all these processes, thus making the timing of sea ice breakup a useful predictor of pCO2sw variability in the CAA. We calculated an average net oceanic sink of 14 mmol CO2 · m−2 · day−1 for the CAA during the summer and autumn seasons, but caution that a more rigorous budgeting approach is required to fully account for biases in dates and locations of our measurements.
Simulating the Weekly Cycle of NOx‐VOC‐HOx‐O3 Photochemical System in the South Coast of California During CalNex‐2010 Campaign
Authors: Cai Chenxia , Avise Jeremy , Kaduwela Ajith , DaMassa John , Warneke Carsten , Gilman Jessica B. , Kuster William , de Gouw Joost , Volkamer Rainer , Stevens Philip , Lefer Barry , Holloway John S. , Pollack Ilana B. , Ryerson Thomas , Atlas Elliot , Blake Donald , Rappenglueck Bernhard , Brown Steven S. , Dube William P.
Published: February 2019

United States Environmental Protection Agency guidance on the use of photochemical models for assessing the efficacy of an emissions control strategy for ozone requires that modeling be used in a relative sense. Consequently, testing a modeling system's ability to predict changes in ozone resulting from emission changes is critical. We evaluate model simulations for precursor species (NOx, CO, and volatile organic compounds [VOCs]), radicals (OH and HO2), a secondary pollutant (O3), and the model response of these compounds to weekend/weekday emission changes during California Nexus study in 2010. The modeling system correctly simulated the broad spatial and temporal variation of NOx and O3 in California South Coast. Although the model generally underpredicted the daytime mixing ratios of NO2 at the surface and overpredicted the NO2 column, the simulated weekend to weekday ratios are consistent with each other and match the observed ratios well. The modeling system exhibited reasonable performance in simulating the VOC compounds with fossil fuel origins but has larger bias in simulating certain species associated with noncombustion sources. The modeling system successfully captured the weekend changes of the enhancement ratios for various VOC species to CO and the relative changes of HOx, which are indicators of faster chemical processing on weekends. This work demonstrates satisfactory model performances for O3 and most relevant chemical compounds with more robust performance in simulating weekend versus weekday changes. Improved planetary boundary layer height simulations, a better understanding of OH‐HO2 cycling, continued improvement of emissions, especially urban biogenic emissions and emissions of oxygenated VOCs, are important for future model improvement.
Parameter Analysis and Estimates for the MODIS Evapotranspiration Algorithm and Multiscale Verification
Authors: Zhang Kun , Zhu Gaofeng , Ma Jinzhu , Yang Yuting , Shang Shasha , Gu Chunjie
Published: February 2019

Accurate estimation of terrestrial evapotranspiration (E) is critical to understand the world's energy and water cycles. MOD16 is the core algorithm of the widely used global E data set (the Moderate Resolution Imaging Spectroradiometer [MODIS] E product). However, it exhibits considerable uncertainties in some regions. Based on the data from 175 flux towers, we identified the key parameters of the MOD16 algorithm using the Sobol’ sensitivity analysis method across biomes. The output of the MOD16 algorithm was sensitive to eight parameters. Among them, β, which is treated as a constant (0.2 kPa) across biomes in the original MOD16 algorithm, was identified as the parameter to which the algorithm was most sensitive. We used the differential‐evolution Markov chain method to obtain the proper posterior distributions for each key parameter across a range of biomes. The values of the key parameters for the different biomes were accurately estimated by differential‐evolution Markov chain in comparison with data from the flux towers. We then evaluated the performances of the original MOD16 and the optimized MOD16 and compared them at multiple spatial scales (i.e., site, catchment, and global). We obtained relatively consistent and more reliable E simulations using the optimized MOD16 at all three scales. In the future, more attention should be paid to uncertainties in the algorithm's structure and its parameterizations of soil moisture constraint, canopy resistance, and energy partitioning.
A CFD‐Based Mixing Model for Vegetated Flows
Authors: Sonnenwald F. , Guymer I. , Stovin V.
Published: February 2019

This paper provides a computational fluid dynamics (CFD)‐based modeling framework for predicting flow field, turbulence, and mixing characteristics within vegetated environments such as ponds and wetlands. The framework has been implemented within a commercial CFD code—ANSYS Fluent 19—via a set of user‐defined functions. Following the approach outlined by King et al. (2012, https://doi.org/10.1017/jfm.2012.113), the standard k‐ε turbulence closure model has been modified to capture the energy transfer at the vegetation/clear flow shear interface and within the vegetation. The implementation assumes that vegetation is vertical, but nonorthogonal flow in the horizontal plane is accounted for. Values for the drag coefficient and the mixing coefficients are estimated based on the vegetation stem diameter and density. Following Tanino and Nepf (2008, https://doi.org/10.1017/S0022112008000505), a switch has been incorporated to account for the fact that the relevant length scale changes from stem diameter to stem spacing as stem density increases. A set of model parameters is proposed, based on a reevaluation of previously published laboratory data and theoretical analysis. Five different experimental data sets are used to demonstrate that the model is able to predict mixing within fully vegetated systems and due to both vertical and horizontal shear layers. The framework was developed to provide a practical prediction tool for engineering purposes, in particular for the estimation of residence time distributions in real partially vegetated stormwater management ponds. Its implementation here within a commercial CFD package potentially facilitates application to complex pond geometries, including patches of different types of vegetation with different bulk stem diameter and density characteristics.
Extending the Record of Surface Melt on the Larsen C Ice Shelf
Authors: Cook Terri
Published: February 2019

The first use of Advanced Scatterometer radar data to determine melt duration on an Antarctic ice shelf shows the season has decreased by up to 2 days per year during the extended 21st century record.
Podcast: Rifts Beneath the Ocean Floor
Authors: Speiser Joshua
Published: February 2019

In the latest episode of its Centennial series, AGU’s Third Pod from the Sun features the pioneering work of a deep-sea explorer.
Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth
Authors: Kashiyama Yuichiro , Yokoyama Akiko , Shiratori Takashi , Hess Sebastian , Not Fabrice , Bachy Charles , Gutierrez-Rodriguez Andres , Kawahara Jun , Suzaki Toshinobu , Nakazawa Masami , Ishikawa Takahiro , Maruyama Moe , Wang Mengyun , Chen Man , Gong Yingchun , Seto Kensuke , Kagami Maiko , Hamamoto Yoko , Honda Daiske , Umetani Takahiro , Shihongi Akira , Kayama Motoki , Matsuda Toshiki , Taira Junya , Yabuki Akinori , Tsuchiya Masashi , Hirakawa Yoshihisa , Kawaguchi Akane , Nomura Mami , Nakamura Atsushi , Namba Noriaki , Matsumoto Mitsufumi , Tanaka Tsuyoshi , Yoshino Tomoko , Higuchi Rina , Yamamoto Akihiro , Maruyama Tadanobu , Yamaguchi Aika , Uzuka Akihiro , Miyagishima Shinya , Tanifuji Goro , Kawachi Masanobu , Kinoshita Yusuke , Tamiaki Hitoshi
Published: February 2019

Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 132,173-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation.
Elevated IgM and abnormal free light chain ratio are increased in relatives from high-risk chronic lymphocytic leukemia pedigrees
Authors: Glenn Martha J. , Madsen Michael J. , Davis Ethan , Garner Cassandra D. , Curtin Karen , Jones Brandt , Williams Justin A. , Tomasson Michael H. , Camp Nicola J.
Published: February 2019

Abnormal serum immunoglobulin (Ig) free light chains (FLC) are established biomarkers of early disease in multiple B-cell lymphoid malignancies, including chronic lymphocytic leukemia (CLL). Heavy chains have also been shown to be biomarkers in plasma cell disorders. An unanswered question is whether these Ig biomarkers are heritable, i.e., influenced by germline factors. CLL is heritable but highly heterogeneous. Heritable biomarkers could elucidate steps of disease pathogenesis that are affected by germline factors, and may help partition heterogeneity and identify genetic pleiotropies across malignancies. Relatives in CLL pedigrees present an opportunity to identify heritable biomarkers. We compared FLCs and heavy chains between relatives in 23 high-risk CLL pedigrees and population controls. Elevated IgM (eIgM) and abnormal FLC (aFLC) ratio was significantly increased in relatives, suggesting that these Ig biomarkers are heritable and could offer risk stratification in pedigree relatives. Within high-risk CLL pedigrees, B-cell lymphoid malignancies were five times more prevalent in close relatives of individuals with eIgM, prostate cancer was three times more prevalent in relatives of individuals with aFLC, and monoclonal B-cell lymphocytosis increased surrounding individuals with normal Ig levels. These different clustering patterns suggest Ig biomarkers have the potential to partition genetic heterogeneity in CLL and provide insight into distinct heritable pleiotropies associated with CLL.
Room temperature CO2 reduction to solid carbon species on liquid metals featuring atomically thin ceria interfaces
Authors: Esrafilzadeh Dorna , Zavabeti Ali , Jalili Rouhollah , Atkin Paul , Choi Jaecheol , Carey Benjamin J. , Brkljača Robert , O’Mullane Anthony P. , Dickey Michael D. , Officer David L. , MacFarlane Douglas R. , Daeneke Torben , Kalantar-Zadeh Kourosh
Published: February 2019

Negative carbon emission technologies are critical for ensuring a future stable climate. However, the gaseous state of CO2 does render the indefinite storage of this greenhouse gas challenging. Herein, we created a liquid metal electrocatalyst that contains metallic elemental cerium nanoparticles, which facilitates the electrochemical reduction of CO2 to layered solid carbonaceous species, at a low onset potential of −310 mV vs CO2/C. We exploited the formation of a cerium oxide catalyst at the liquid metal/electrolyte interface, which together with cerium nanoparticles, promoted the room temperature reduction of CO2. Due to the inhibition of van der Waals adhesion at the liquid interface, the electrode was remarkably resistant to deactivation via coking caused by solid carbonaceous species. The as-produced solid carbonaceous materials could be utilised for the fabrication of high-performance capacitor electrodes. Overall, this liquid metal enabled electrocatalytic process at room temperature may result in a viable negative emission technology.
Impact of pre-existing dengue immunity on human antibody and memory B cell responses to Zika
Authors: Andrade Paulina , Gimblet-Ochieng Ciara , Modirian Faraz , Collins Matthew , Cárdenas Maritza , Katzelnick Leah C. , Montoya Magelda , Michlmayr Daniela , Kuan Guillermina , Balmaseda Angel , Coloma Josefina , de Silva Aravinda M. , Harris Eva
Published: February 2019

Little is known about enduring memory B cell (MBC) responses to Zika virus (ZIKV) and their relationship with circulating antibodies. Here we comprehensively assess MBC frequency and specificity alongside serum binding and neutralizing antibody responses to ZIKV ~2 weeks and ~8 months postinfection in 31 pediatric subjects with 0, 1 or >1 prior infections with the related dengue virus (DENV). ZIKV infection elicits a robust type-specific MBC response, and the majority of late convalescent anti-ZIKV serum neutralizing activity is attributable to ZIKV-specific antibodies. The number of prior DENV infections does not influence type-specific or cross-reactive MBC responses, although ZIKV has the highest cross-reactivity with DENV3. DENV cross-reactive MBCs expanded by ZIKV infection decline in number and proportion by late convalescence. Finally, ZIKV induces greater cross-reactivity in the MBC pool than in serum antibodies. Our data suggest immunity to DENV only modestly shapes breadth and magnitude of enduring ZIKV antibody responses.
Experimental crossbreeding reveals strain-specific variation in mortality, growth and personality in the brown trout (Salmo trutta)
Authors: Ågren Anni , Vainikka Anssi , Janhunen Matti , Hyvärinen Pekka , Piironen Jorma , Kortet Raine
Published: February 2019

Although hybridization between populations with low genetic diversity may induce heterosis, it can also lead to reduced fitness of hybrid offspring through outbreeding depression and loss of local adaptations. Using a half-sib mating design, we studied on brown trout (Salmo trutta) how hybridization of migratory hatchery-strain females with males from various strains would affect early mortality, growth and personality in F1 offspring. No differences in mortality or alevin body length were found between the crossing groups by the end of the yolk-sac stage. At later developmental stages, higher mortality and slower growth in one of the geographically distant hybrid groups indicated potential outbreeding depression. The personality component indicating boldness and exploration tendency showed fairly low genetic variation and no phenotypic differences among the crossing groups while the personality component related to freezing behavior indicated stronger freezing responses in the purebred and local cross strain when compared to the two other strains. However, the purebred hatchery strain possessed stronger additive genetic tendency for boldness and explorative behavior, and weaker genetic tendency for freezing behavior, when compared to the wild × hatchery hybrid group. Our results add to the cumulating evidence of risks related to the stocking of fish strains from non-native origins.
Randomized controlled trial on the influence of dietary intervention on epigenetic mechanisms in children with cow’s milk allergy: the EPICMA study
Authors: Paparo Lorella , Nocerino Rita , Bruno Cristina , Di Scala Carmen , Cosenza Linda , Bedogni Giorgio , Di Costanzo Margherita , Mennini Maurizio , D’Argenio Valeria , Salvatore Francesco , Berni Canani Roberto
Published: February 2019

Epigenetic mechanisms could drive the disease course of cow’s milk allergy (CMA) and formula choice could modulate these pathways. We compared the effect of two different dietary approaches on epigenetic mechanisms in CMA children. Randomized controlled trial on IgE-mediated CMA children receiving a 12-month treatment with extensively hydrolyzed casein formula containing the probiotic L.rhamnosus GG (EHCF + LGG) or with soy formula (SF). At the baseline, after 6 and 12 months of treatment FoxP3 methylation rate and its expression in CD4+ T cells were assessed. At same study points IL-4, IL-5, IL-10, and IFN-γ methylation rate, expression and serum concentration, miRNAs expression were also investigated. 20 children (10/group) were evaluated. Baseline demographic, clinical and epigenetic features were similar in the two study groups. At 6 and 12 months, EHCF + LGG group showed a significant increase in FoxP3 demethylation rate compared to SF group. At the same study points, EHCF + LGG group presented a higher increase in IL-4 and IL-5 and a higher reduction in IL-10 and IFN-γ DNA methylation rate compared to SF group. A different modulation of miR-155, -146a, -128 and -193a expression was observed in EHCF + LGG vs. SF. Dietary intervention could exert a different epigenetic modulation on the immune system in CMA children.
Single step fabrication of Silicon resistors on SOI substrate used as Thermistors
Authors: Rollo Serena , Rani Dipti , Olthuis Wouter , Pascual García César
Published: February 2019

Temperature sensing is one of the important features of Micro Electro Mechanical Systems and a monolithic integration provides advantages for both fabrication simplicity and performance. The use of Silicon On Insulator substrates allows simple fabrication of integrated wires that can be used as thermistors. We fabricated rectangular and triangular silicon wires with different dimensions in a single step fabrication process based on the wet etching of a <110> Silicon On Insulator substrate. We determined the experimental resistivity of the two kinds of devices and tested their performance as thermistors in a temperature range between 24 and 100 °C. The accuracy and normalized sensitivities of our devices were 0.4 °C and 0.3–0.5%/°C, respectively. The potential of the proposed method resides in the possibility of having devices with different shapes in a single straightforward process.
Integrative analysis of postharvest chilling injury in cherry tomato fruit reveals contrapuntal spatio-temporal responses to ripening and cold stress
Authors: Albornoz Karin , Cantwell Marita I. , Zhang Lu , Beckles Diane M.
Published: February 2019

Postharvest chilling injury (PCI) reduces fruit quality and shelf-life in tomato (Solanum lycopersicum L.). PCI has been traditionally studied in the pericarp, however its development is likely heterogeneous in different fruit tissues. To gain insight into PCI’s spatio-temporal development, we used postharvest biomarkers e.g. respiration and ethylene rates, ion leakage etc., to confirm the occurrence of PCI, and compared these data with molecular (gene expression), biophysical (MRI data) and biochemical parameters (Malondialdehyde (MDA) and starch content) from the pericarp or columella. Tissues were stored at control (12.5 °C) or PCI-inducing temperatures (2.5 or 5 °C) followed by rewarming at 20 °C. MRI and ion leakage revealed that cold irreversibly impairs ripening-associated membrane liquefaction; MRI also showed that the internal and external fruit tissues responded differently to cold. MDA and especially starch contents, were affected by chilling in a tissue-specific manner. The expression of the six genes studied: ACO1 and ACS2 (ripening), CBF1 (cold response), DHN, AOX1a and LoxB (stress-related) showed non-overlapping temporal and spatially-specific responses. Overall, the data highlighted the interconnectedness of fruit cold response and ripening, and showed how cold stress reconfigures the latter. They further underscored that multidimensional spatial and temporal biological studies are needed to develop effective solutions to PCI.
Short-term and long-term effects of low serum bicarbonate level at admission in hospitalised patients
Authors: Lim Sung Yoon , Park Youngmi , Chin Ho Jun , Na Ki Young , Chae Dong-Wan , Kim Sejoong
Published: February 2019

Although low serum bicarbonate level is known to be associated with adverse outcomes in patients with chronic kidney injury, it is unclear whether low serum bicarbonate level is associated with the development of acute kidney injury (AKI). The purpose of our study was to determine whether serum bicarbonate levels at admission could be a risk factor for AKI development and mortality in hospitalised patients. We retrospectively enrolled 17,320 adult patients who were admitted to the academic teaching hospital from January 2013 to December 2013. Patients were divided into 2 groups based on the first measurement of serum bicarbonate level at admission. The incidence of AKI was higher in patients with low serum bicarbonate level than in those with normal serum bicarbonate level (8.0% vs. 4.1%). Low serum bicarbonate levels at admission were significantly associated with the development of AKI. In addition, low serum bicarbonate levels also independently predicted the 90-day mortality. Pre-existing low bicarbonate levels and subsequent development of AKI increased in-hospital mortality by 15 times compared with that in patients with normal bicarbonate levels and no AKI. Low serum bicarbonate levels may be associated with the development of AKI and high mortality in hospitalised patients.
Early differentiation of long-standing persistent atrial fibrillation using the characteristics of fibrillatory waves in surface ECG multi-leads
Authors: Park Junbeom , Lee Chungkeun , Leshem Eran , Blau Ira , Kim Sungsoo , Lee Jung Myung , Hwang Jung-A , Choi Byung-il , Lee Moon-Hyoung , Hwang Hye Jin
Published: February 2019

We characterized the f-waves in atrial fibrillation (AF) in the surface ECG by quantifying the amplitude, irregularity, and dominant rate of the f-waves in leads II, aVL, and V1, and investigated whether those parameters of the f-waves could discriminate long-standing persistent AF (LPeAF) from non-LPeAF. A total of 224 AF patients were enrolled: 112 with PAF (87 males), 48 with PeAF (38 males), and 64 with LPeAF (47 males). The f-waves in surface ECG leads V1, aVL, and II, which reflect well electrical activity in the right atrium (RA), the left atrium (LA), and both atria, respectively, were analyzed. The f-waves for LPeAF had lower amplitudes in II and aVL, increased irregularity and a higher dominant rate in II and V1 compared to PAF and PeAF (all p < 0.02). In a multivariate analysis, a low amplitude in lead II (<34.6 uV) and high dominant rate in lead V1 (≧390/min) (p < 0.001) independently discriminated LPeAF from the other AF types. The f-waves combined with both a low amplitude in lead II and high dominant rate in lead V1 were significantly associated with LPeAF (OR 6.27, p < 0.001). Characteristics of the f-waves on the surface ECG could discriminate LPeAF from other types of AF.
Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress
Authors: Catacchio C. R. , Alagna F. , Perniola R. , Bergamini C. , Rotunno S. , Calabrese F. M. , Crupi P. , Antonacci D. , Ventura M. , Cardone M. F.
Published: February 2019

Grapevine (Vitis vinifera L.) is importantly cultivated worldwide for table grape and wine production. Its cultivation requires irrigation supply, especially in arid and semiarid areas. Water deficiency can affect berry and wine quality mostly depending on the extent of plant perceived stress, which is a cultivar-specific trait. We tested the physiological and molecular responses to water deficiency of two table grape cultivars, Italia and Autumn royal, and we highlighted their different adaptation. Microarray analyses revealed that Autumn royal reacts involving only 29 genes, related to plant stress response and ABA/hormone signal transduction, to modulate the response to water deficit. Instead, cultivar Italia orchestrates a very broad response (we found 1037 differentially expressed genes) that modifies the cell wall organization, carbohydrate metabolism, response to reactive oxygen species, hormones and osmotic stress. For the first time, we integrated transcriptomic data with cultivar-specific genomics and found that ABA-perception and –signalling are key factors mediating the varietal-specific behaviour of the early response to drought. We were thus able to isolate candidate genes for the genotype-dependent response to drought. These insights will allow the identification of reliable plant stress indicators and the definition of sustainable cultivar-specific protocols for water management.
Serum biomarkers identification by iTRAQ and verification by MRM: S100A8/S100A9 levels predict tumor-stroma involvement and prognosis in Glioblastoma
Authors: Arora Anjali , Patil Vikas , Kundu Paramita , Kondaiah Paturu , Hegde A. S. , Arivazhagan A. , Santosh Vani , Pal Debnath , Somasundaram Kumaravel
Published: February 2019

Despite advances in biology and treatment modalities, the prognosis of glioblastoma (GBM) remains poor. Serum reflects disease macroenvironment and thus provides a less invasive means to diagnose and monitor a diseased condition. By employing 4-plex iTRAQ methodology, we identified 40 proteins with differential abundance in GBM sera. The high abundance of serum S100A8/S100A9 was verified by multiple reaction monitoring (MRM). ELISA and MRM-based quantitation showed a significant positive correlation. Further, an integrated investigation using stromal, tumor purity and cell type scores demonstrated an enrichment of myeloid cell lineage in the GBM tumor microenvironment. Transcript levels of S100A8/S100A9 were found to be independent poor prognostic indicators in GBM. Medium levels of pre-operative and three-month post-operative follow-up serum S100A8 levels predicted poor prognosis in GBM patients who lived beyond median survival. In vitro experiments showed that recombinant S100A8/S100A9 proteins promoted integrin signalling dependent glioma cell migration and invasion up to a threshold level of concentrations. Thus, we have discovered GBM serum marker by iTRAQ and verified by MRM. We also demonstrate interplay between tumor micro and macroenvironment and identified S100A8 as a potential marker with diagnostic and prognostic value in GBM.
Very High Refractive Index Transition Metal Dichalcogenide Photonic Conformal Coatings by Conversion of ALD Metal Oxides
Authors: Chen Christopher T. , Pedrini Jacopo , Gaulding E. Ashley , Kastl Christoph , Calafiore Giuseppe , Dhuey Scott , Kuykendall Tevye R. , Cabrini Stefano , Toma Francesca M. , Aloni Shaul , Schwartzberg Adam M.
Published: February 2019

Materials for nanophotonic devices ideally combine ease of deposition, very high refractive index, and facile pattern formation through lithographic templating and/or etching. In this work, we present a scalable method for producing high refractive index WS2 layers by chemical conversion of WO3 synthesized via atomic layer deposition (ALD). These conformal nanocrystalline thin films demonstrate a surprisingly high index of refraction (n > 3.9), and structural fidelity compatible with lithographically defined features down to ~10 nm. Although this process yields highly polycrystalline films, the optical constants are in agreement with those reported for single crystal bulk WS2. Subsequently, we demonstrate three photonic structures - first, a two-dimensional hole array made possible by patterning and etching an ALD WO3 thin film before conversion, second, an analogue of the 2D hole array first patterned into fused silica before conformal coating and conversion, and third, a three-dimensional inverse opal photonic crystal made by conformal coating of a self-assembled polystyrene bead template. These results can be trivially extended to other transition metal dichalcogenides, thus opening new opportunities for photonic devices based on high refractive index materials.
Glyoxylate cycle gene ICL1 is essential for the metabolic flexibility and virulence of Candida glabrata
Authors: Chew Shu Yih , Ho Kok Lian , Cheah Yoke Kqueen , Ng Tzu Shan , Sandai Doblin , Brown Alistair J. P. , Than Leslie Thian Lung
Published: February 2019

The human fungal pathogen Candida glabrata appears to utilise unique stealth, evasion and persistence strategies in subverting the onslaught of host immune response during systemic infection. However, macrophages actively deprive the intracellular fungal pathogen of glucose, and therefore alternative carbon sources probably support the growth and survival of engulfed C. glabrata. The present study aimed to investigate the role of the glyoxylate cycle gene ICL1 in alternative carbon utilisation and its importance for the virulence of C. glabrata. The data showed that disruption of ICL1 rendered C. glabrata unable to utilise acetate, ethanol or oleic acid. In addition, C. glabrata icl1∆ cells displayed significantly reduced biofilm growth in the presence of several alternative carbon sources. It was also found that ICL1 is crucial for the survival of C. glabrata in response to macrophage engulfment. Disruption of ICL1 also conferred a severe attenuation in the virulence of C. glabrata in the mouse model of invasive candidiasis. In conclusion, a functional glyoxylate cycle is essential for C. glabrata to utilise certain alternative carbon sources in vitro and to display full virulence in vivo. This reinforces the view that antifungal drugs that target fungal Icl1 have potential for future therapeutic intervention.
Early postoperative hypoalbuminaemia is associated with pleural effusion after donor hepatectomy: A propensity score analysis of 2316 donors
Authors: Jeong Hye-Won , Kim Jung-Won , Shin Won-Jung , Kim Seon-Ok , Moon Young-Jin , Kwon Hye-Mee , Jung Kyeo-Woon , Jun In-Gu , Song Jun-Gol , Hwang Gyu-Sam
Published: February 2019

Pleural effusion and hypoalbuminaemia frequently occur after hepatectomy. Despite the emphasis on the safety of donors, little is known about the impact of postoperative albumin level on pleural effusion in liver donors. We retrospectively assessed 2316 consecutive liver donors from 2004 to 2014. The analysis of donors from 2004 to 2012 showed that postoperative pleural effusion occurred in 47.4% (970/2046), and serum albumin levels decreased until postoperative day 2 (POD2) and increased thereafter. In multivariable analysis, the lowest albumin level within POD2 (POD2ALB) was inversely associated with pleural effusion (OR 0.28, 95% CI 0.20–0.38; P < 0.001). POD2ALB ≤3.0 g/dL, the cutoff value at the 75th percentile, was associated with increased incidence of pleural effusion after propensity score (PS) matching (431 pairs; OR 1.69, 95% CI 1.30–2.21; P < 0.001). When we further analysed data from 2010 to 2014, intraoperative albumin infusion was associated with higher POD2ALB (P < 0.001) and lower incidence of pleural effusion (P = 0.024), compared with synthetic colloid infusion after PS matching (193 pairs). In conclusion, our data showed that POD2ALB is inversely associated with pleural effusion, and that intraoperative albumin infusion is associated with a lower incidence of pleural effusion when compared to synthetic colloid infusion in liver donors.
Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning
Authors: O’Brien Aidan R. , Wilson Laurence O. W. , Burgio Gaetan , Bauer Denis C.
Published: February 2019

Editing individual nucleotides is a crucial component for validating genomic disease association. It is currently hampered by CRISPR-Cas-mediated “base editing” being limited to certain nucleotide changes, and only achievable within a small window around CRISPR-Cas target sites. The more versatile alternative, HDR (homology directed repair), has a 3-fold lower efficiency with known optimization factors being largely immutable in experiments. Here, we investigated the variable efficiency-governing factors on a novel mouse dataset using machine learning. We found the sequence composition of the single-stranded oligodeoxynucleotide (ssODN), i.e. the repair template, to be a governing factor. Furthermore, different regions of the ssODN have variable influence, which reflects the underlying mechanism of the repair process. Our model improves HDR efficiency by 83% compared to traditionally chosen targets. Using our findings, we developed CUNE (Computational Universal Nucleotide Editor), which enables users to identify and design the optimal targeting strategy using traditional base editing or – for-the-first-time – HDR-mediated nucleotide changes.