bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrodynamics of the Po River‐Delta‐Sea System
Authors: Maicu Francesco , De Pascalis Francesca , Ferrarin Christian , Umgiesser Georg 
Published: July 2018

AbstractIn this study we investigated the hydrodynamics and the interaction between riverine and marine waters in the Po River‐Delta‐Sea (RDS) system (Italy). Through the application of an unstructured 3D numerical model to a domain comprising the Po river branches, seven coastal lagoons and the shelf sea, many of the hydrodispersive phenomena evolving from the interaction of the different water bodies of the RDS system were described. The model was successfully calibrated and validated for water levels, fluxes at the inlets and at the river branches, and water temperature and salinity observations. The use of such a comprehensive approach allows the characterization of the general hydrodynamics of all the components of the Po RDS system, of the water exchange between different water bodies as well as the Po river discharge distribution among all branches. The analysis of calculated coastal current patterns in the prodelta of two different years and during a flood event confirms that the Po River is the main driver of the baroclinic coastal sea circulation. However, when strong winds occur (Sirocco and Bora), the surficial circulation of the shelf area is significantly modified. Generally, the lagoons of the Po RDS system can be considered hydrodynamically active since their tidal prisms represent a relevant fraction of each lagoon's volume. The natural consequence is that the lagoons show an active flushing with water renewal times in the order of few days. The hydrodynamics is mainly forced by the tide and is locally enhanced by riverine inputs and wind. Where freshwater inputs are significant, they are responsible of the lagoons salinity patterns that show high spatial gradients (not all the lagoons are well mixed) and temporal variability. The variability of the freshwater discharges and the complex morphology of the Po RDS allows the presence of both marine and riverine environments.
Accounting for Changing Temperature Patterns Increases Historical Estimates of Climate Sensitivity
Authors: Andrews Timothy , Gregory Jonathan M. , Paynter David , Silvers Levi G. , Zhou Chen , Mauritsen Thorsten , Webb Mark J. , Armour Kyle C. , Forster Piers M. , Titchner Holly 
Published: July 2018

AbstractEight atmospheric general circulation models (AGCMs) are forced with observed historical (1871–2010) monthly sea surface temperature and sea ice variations using the Atmospheric Model Intercomparison Project II data set. The AGCMs therefore have a similar temperature pattern and trend to that of observed historical climate change. The AGCMs simulate a spread in climate feedback similar to that seen in coupled simulations of the response to CO2 quadrupling. However, the feedbacks are robustly more stabilizing and the effective climate sensitivity (EffCS) smaller. This is due to a pattern effect, whereby the pattern of observed historical sea surface temperature change gives rise to more negative cloud and longwave clear‐sky feedbacks. Assuming the patterns of long‐term temperature change simulated by models, and the radiative response to them, are credible; this implies that existing constraints on EffCS from historical energy budget variations give values that are too low and overly constrained, particularly at the upper end. For example, the pattern effect increases the long‐term Otto et al. (2013, https://doi.org/10.1038/ngeo1836) EffCS median and 5–95% confidence interval from 1.9 K (0.9–5.0 K) to 3.2 K (1.5–8.1 K).
Plant Traits are Key Determinants in Buffering the Meteorological Sensitivity of Net Carbon Exchanges of Arctic Tundra
Authors: López‐Blanco Efrén , Lund Magnus , Christensen Torben R. , Tamstorf Mikkel P. , Smallman Thomas L. , Slevin Darren , Westergaard‐Nielsen Andreas , Hansen Birger U. , Abermann Jakob , Williams Mathew 
Published: July 2018

AbstractThe climate sensitivity of carbon (C) cycling in Arctic terrestrial ecosystems is a major unknown in the Earth system. There is a lack of knowledge about the mechanisms that drive the interactions between photosynthesis, respiration, and changes in C stocks across full annual cycles in Arctic tundra. We use a calibrated and validated model (soil‐plant‐atmosphere; SPA) to estimate net ecosystem exchange (NEE), gross primary production (GPP), ecosystem respiration (Reco), and internal C processing across eight full years. SPA's carbon flux estimates are validated with observational data obtained from the Greenland Ecosystem Monitoring program in West Greenland tundra. Overall, the model explained 73%, 73%, and 50% of the variance in NEE, GPP, and Reco, respectively, and 85% of the plant greenness variation. Flux data highlighted the insensitivity of growing season NEE to interannual meteorological variability, due to compensatory responses of photosynthesis and ecosystem respiration. In this modelling study, we show that this NEE buffering is the case also for full annual cycles. We show through a sensitivity analysis that plant traits related to nitrogen are likely key determinants in the compensatory response, through simulated links to photosynthesis and plant respiration. Interestingly, we found a similar temperature sensitivity of the trait‐flux couplings for GPP and Reco, suggesting that plant traits drive the stabilization of NEE. Further, model analysis indicated that wintertime periods decreased the C sink by 60%, mostly driven by litter heterotrophic respiration. This result emphasizes the importance of wintertime periods and allows a more comprehensive understanding of full annual C dynamics.
Nitrogen Fixation Occurring in Sediments: Contribution to the Nitrogen Budget of Lake Taihu, China
Authors: Yao Xiaolong , Zhang Lu , Zhang Yunlin , Zhang Bo , Zhao Zhonghua , Zhang Yibo , Li Min , Jiang Xingyu 
Published: July 2018

AbstractNitrogen fixation (N2 fixation) in benthic sediment contributes a certain amount of bioavailable nitrogen (N) to aquatic systems. However, data on sediment N2 fixation have been poorly documented and the contribution of sediment N2 fixation to the N budget in lakes has rarely been studied. In this study, N2 fixation rates in sediments of Lake Taihu were measured periodically using the traditional acetylene reduction assay. Results showed that the highest sediment N2 fixation rate occurred in winter in Meiliang Bay, with a value of 258 nmol N·kg−1·hr−1, and the lowest rates occurred in all seasons at some sites, with values near zero. East Taihu Bay, Meiliang Bay, the southwestern coastal area, and Zhushan Bay were found to be hotspots for sediment N2 fixation activity. The annual N2 fixation rate and volume in sediments of Lake Taihu were 0.083 g N·m−2·year−1 and 195 t N, respectively. The N inputs via fixation were much lower than those from river inflow, sediment release, and atmospheric deposition. This study reveals that N2 fixation in sediments contributes only a minor part to the overall N budget, while it compensates for about 1.8% of sediment N2 loss via denitrification. The minor contribution of sediment N2 fixation to the overall N budget in Lake Taihu may be closely linked to sediment characteristics.
Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms
Authors: Unfried Frank , Becker Stefan , Robb Craig S , Hehemann Jan-Hendrik , Markert Stephanie , Heiden Stefan E , Hinzke Tjorven , Becher Dörte , Reintjes Greta , Krüger Karen , Avcı Burak , Kappelmann Lennart , Hahnke Richard L , Fischer Tanja , Harder Jens , Teeling Hanno , Fuchs Bernhard , Barbeyron Tristan , Amann Rudolf I , Schweder Thomas 
Published: July 2018

Abstract
Polysaccharide degradation by heterotrophic microbes is a key process within Earth’s carbon cycle. Here, we use environmental proteomics and metagenomics in combination with cultivation experiments and biochemical characterizations to investigate the molecular details of in situ polysaccharide degradation mechanisms during microalgal blooms. For this, we use laminarin as a model polysaccharide. Laminarin is a ubiquitous marine storage polymer of marine microalgae and is particularly abundant during phytoplankton blooms. In this study, we show that highly specialized bacterial strains of the Bacteroidetes phylum repeatedly reached high abundances during North Sea algal blooms and dominated laminarin turnover. These genomically streamlined bacteria of the genus Formosa have an expanded set of laminarin hydrolases and transporters that belonged to the most abundant proteins in the environmental samples. In vitro experiments with cultured isolates allowed us to determine the functions of in situ expressed key enzymes and to confirm their role in laminarin utilization. It is shown that laminarin consumption of Formosa spp. is paralleled by enhanced uptake of diatom-derived peptides. This study reveals that genome reduction, enzyme fusions, transporters, and enzyme expansion as well as a tight coupling of carbon and nitrogen metabolism provide the tools, which make Formosa spp. so competitive during microalgal blooms.
Phase 1/2 trial of ixazomib, cyclophosphamide and dexamethasone in patients with previously untreated symptomatic multiple myeloma
Authors: Kumar Shaji K. , Buadi Francis K. , LaPlant Betsy , Halvorson Alese , Leung Nelson , Kapoor Prashant , Dingli David , Gertz Morie A. , Go Ronald S. , Bergsagel P. Leif , Lin Yi , Dispenzieri Angela , Hwa Yi Lisa , Fonder Amie , Hobbs Miriam , Fonseca Rafael , Hayman Suzanne R. , Stewart A. Keith , Lust John A. , Mikhael Joseph , Gonsalves Wilson , Reeder Craig , Skacel Tomas , Rajkumar S. Vincent , Lacy Martha Q. 
Published: July 2018

AbstractIxazomib is the first oral proteasome inhibitor to enter the clinic. Given the efficacy of bortezomib in combination with cyclophosphamide and dexamethasone, we studied the combination of ixazomib, cyclophosphamide and dexamethasone (ICd) in newly diagnosed multiple myeloma (NDMM) and patients with measurable disease, irrespective of transplant eligibility, were enrolled. The phase 1 was to determine the maximum tolerated dose (MTD) of cyclophosphamide in the combination. Patients received ixazomib 4 mg (days 1, 8, 15), dexamethasone 40 mg (days 1, 8, 15, 22), and cyclophosphamide 300 or 400 mg/m2 days 1, 8, 15, 22; cycles were 28 days. We enrolled 51 patients, 10 in phase 1 and 41 patients in phase 2. The median age was 64.5 years (range: 41–88); 29% had high or intermediate risk FISH. The MTD was 400 mg/m2 of cyclophosphamide weekly. The best confirmed response in all 48 patients included ≥ partial response in 77%, including ≥ VGPR in 35%; 3 patients had a sCR. The response rate for all 48 evaluable patients at 4-cycles was 71%; the median time to response was 1.9 months. Common adverse events included cytopenias, fatigue and GI intolerance. ICd is a convenient, all oral combination that is well tolerated and effective in NDMM.
TiO2 nanoparticles assembled on kaolinites with different morphologies for efficient photocatalytic performance
Authors: Li Xiaoyu , Peng Kang , Chen Huaxin , Wang Zhenjun 
Published: July 2018

AbstractNatural kaolinite clays with different dimensionalities (including kaolinite nanoflakes and nanorods) supported TiO2 nanoparticles were successfully prepared via a facile sol-gel method. Moreover, comparisons between FK/TiO2 and RK/TiO2 nanocomposites are conducted in terms of matrix morphology, surface property, energy band structure and interfacial interaction. The effects of kaolinite microstructure, morphology and dimensionality on the interfacial characteristics and photocatalytic properties of the nanocomposites were investigated in detail. The results showed that TiO2 nanoparticles are more easily attached on the kaolinite nanoflakes, and possess more uniform distribution and smaller particle size than that of kaolinite nanorods. In particular, the FK/TiO2 nanocatalysts exhibit higher photocatalytic activity for the degradation of tetracycline hydrochloride than that of RK/TiO2 and bare TiO2, which is attributed to the stronger surface adsorptivity, higher loading efficiency and smaller grain size. Additionally, FK/TiO2 composites show excellent stability, which is ascribed to the intimate interfacial contact between two-dimensional kaolinite nanoflakes and TiO2 nanoparticles. Overall, the enhanced catalytic performance for FK/TiO2 composites is the synergistic effect of two-dimensional morphology, better adsorption capability and more active photocatalysis TiO2 species.
Impaired HDL cholesterol efflux capacity in patients with non-alcoholic fatty liver disease is associated with subclinical atherosclerosis
Authors: Fadaei Reza , Poustchi Hossein , Meshkani Reza , Moradi Nariman , Golmohammadi Taghi , Merat Shahin 
Published: July 2018

AbstractNon-alcoholic fatty liver disease (NAFLD) is associated with a substantial increased risk of atherosclerotic cardiovascular disease (ASCVD), which is partly related to dyslipidemia and low HDL-C level. The cardioprotective activity of HDL in the body is closely connected to its role in promoting cholesterol efflux, which is determined by cholesterol efflux capacity (CEC). Hitherto, the role of HDL, as defined by CEC has not been assessed in NAFLD patients. In this research study, we present the results of a study of cAMP-treated J774 CEC and THP-1 macrophage CEC in ApoB-depleted plasma of 55 newly diagnosed NAFLD patients and 30 controls. Circulating levels of ApoA-I, ApoB, preβ-HDL, plasma activity of CETP, PLTP, LCAT and carotid intima-media thickness (cIMT) were estimated. cAMP-treated J774 and THP-1 macrophage CEC were found to be significantly lower in NAFLD patients compared to controls (P < 0.001 and P = 0.003, respectively). In addition, it was discovered that both ApoA-I and preβ1-HDL were significantly lower in NAFLD patients (P < 0.001). Furthermore, cAMP-treated J774 CEC showed independent negative correlation with cIMT, as well as the presence of atherosclerotic plaque in NAFLD patients. In conclusion, our findings showed that HDL CEC was suppressed in NAFLD patients, and impaired cAMP-treated J774 CEC was an independent risk factor for subclinical atherosclerosis in NAFLD patients, suggesting that impaired HDL functions as an independent risk factor for atherosclerosis in NAFLD.
Learning the meaning of new stimuli increases the cross-correlated activity of prefrontal neurons
Authors: Nougaret Simon , Genovesio Aldo 
Published: July 2018

AbstractThe prefrontal cortex (PF) has a key role in learning rules and generating associations between stimuli and responses also called conditional motor learning. Previous studies in PF have examined conditional motor learning at the single cell level but not the correlation of discharges between neurons at the ensemble level. In the present study, we recorded from two rhesus monkeys in the dorsolateral and the mediolateral parts of the prefrontal cortex to address the role of correlated firing of simultaneously recorded pairs during conditional motor learning. We trained two rhesus monkeys to associate three stimuli with three response targets, such that each stimulus was mapped to only one response. We recorded the neuronal activity of the same neuron pairs during learning of new associations and with already learned associations. In these tasks after a period of fixation, a visual instruction stimulus appeared centrally and three potential response targets appeared in three positions: right, left, and up from center. We found a higher number of neuron pairs significantly correlated and higher cross-correlation coefficients during stimulus presentation in the new than in the familiar mapping task. These results demonstrate that learning affects the PF neural correlation structure.
High-throughput optimisation of light-driven microalgae biotechnologies
Authors: Sivakaminathan Shwetha , Hankamer Ben , Wolf Juliane , Yarnold Jennifer 
Published: July 2018

AbstractMicroalgae biotechnologies are rapidly developing into new commercial settings. Several high value products already exist on the market, and systems development is focused on cost reduction to open up future economic opportunities for food, fuel and freshwater production. Light is a key environmental driver for photosynthesis and optimising light capture is therefore critical for low cost, high efficiency systems. Here a novel high-throughput screen that simulates fluctuating light regimes in mass cultures is presented. The data was used to model photosynthetic efficiency (PEµ, mol photon−1 m2) and chlorophyll fluorescence of two green algae, Chlamydomonas reinhardtii and Chlorella sp. Response surface methodology defined the effect of three key variables: density factor (Df, ‘culture density’), cycle time (tc, ‘mixing rate’), and maximum incident irradiance (Imax). Both species exhibited a large rise in PEµ with decreasing Imax and a minimal effect of tc (between 3–20 s). However, the optimal Df of 0.4 for Chlamydomonas and 0.8 for Chlorella suggested strong preferences for dilute and dense cultures respectively. Chlorella had a two-fold higher optimised PEµ than Chlamydomonas, despite its higher light sensitivity. These results demonstrate species-specific light preferences within the green algae clade. Our high-throughput screen enables rapid strain selection and process optimisation.
Reciprocal Perspective for Improved Protein-Protein Interaction Prediction
Authors: Dick Kevin , Green James R. 
Published: July 2018

AbstractAll protein-protein interaction (PPI) predictors require the determination of an operational decision threshold when differentiating positive PPIs from negatives. Historically, a single global threshold, typically optimized via cross-validation testing, is applied to all protein pairs. However, we here use data visualization techniques to show that no single decision threshold is suitable for all protein pairs, given the inherent diversity of protein interaction profiles. The recent development of high throughput PPI predictors has enabled the comprehensive scoring of all possible protein-protein pairs. This, in turn, has given rise to context, enabling us now to evaluate a PPI within the context of all possible predictions. Leveraging this context, we introduce a novel modeling framework called Reciprocal Perspective (RP), which estimates a localized threshold on a per-protein basis using several rank order metrics. By considering a putative PPI from the perspective of each of the proteins within the pair, RP rescores the predicted PPI and applies a cascaded Random Forest classifier leading to improvements in recall and precision. We here validate RP using two state-of-the-art PPI predictors, the Protein-protein Interaction Prediction Engine and the Scoring PRotein INTeractions methods, over five organisms:Homo sapiens, Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, andMus musculus. Results demonstrate the application of apost hocRP rescoring layer significantly improves classification (p < 0.001) in all cases over all organisms and this new rescoring approach can apply to any PPI prediction method.
Heterotetrameric annexin A2/S100A10 (A2t) is essential for oncogenic human papillomavirus trafficking and capsid disassembly, and protects virions from lysosomal degradation
Authors: Taylor Julia R. , Fernandez Daniel J. , Thornton Shantaé M. , Skeate Joseph G. , Lühen Kim P. , Da Silva Diane M. , Langen Ralf , Kast W. Martin 
Published: July 2018

AbstractHuman papillomavirus (HPV) entry into epithelial cells is independent of canonical endocytic pathways. Upon interaction with host cells, HPV establishes infection by traversing through an endocytic pathway that is clathrin- and caveolin-independent, but dependent on the annexin A2/S100A10 heterotetramer (A2t). We examined the contribution of monomeric annexin A2 (AnxA2) vs. A2t in HPV infection and endocytosis, and further characterized the role of these molecules in protein trafficking. We specifically show that cell surface A2t is not required for HPV attachment, and in the absence of A2t virion internalization remains clathrin-independent. Without A2t, viral progression from early endosomes to multivesicular endosomes is significantly inhibited, capsid uncoating is dramatically reduced, and lysosomal degradation of HPV is accelerated. Furthermore, we present evidence that AnxA2 forms a complex with CD63, a known mediator of HPV trafficking. Overall, the observed reduction in infection is less significant in the absence of S100A10 alone compared to full A2t, supporting an independent role for monomeric AnxA2. More broadly, we show that successful infection by multiple oncogenic HPV types is dependent on A2t. These findings suggest that A2t is a central mediator of high-risk HPV intracellular trafficking post-entry and pre-viral uncoating.
Submarine Groundwater Discharge helps making nearshore waters heterotrophic
Authors: Wang Shu-Lun , Chen Chen-Tung Arthur , Huang Ting-Hsuan , Tseng Hsiao-Chun , Lui Hon-Kit , Peng Tsung-Ren , Kandasamy Selvaraj , Zhang Jing , Yang Liyang , Gao Xuelu , Lou Jiann-Yuh , Kuo Fu-Wen , Chen Xue-Gang , Ye Ying , Lin Yi-Jie 
Published: July 2018

AbstractSubmarine groundwater discharge (SGD) is the submarine seepage of all fluids from coastal sediments into the overlying coastal seas. It has been well documented that the SGD may contribute a great deal of allochthonous nutrients to the coastlines. It is, however, less known how much carbon enters the ocean via the SGD. Nutrients (NO3, NO2, NH4, PO4, SiO2), alkalinity and dissolved inorganic carbon (DIC) in the submarine groundwater were measured at 20 locations around Taiwan for the first time. The total N/P/Si yields from the SGD in Taiwan are respectively 3.28 ± 2.3 × 104, 2.6 ± 1.8 × 102 and 1.89 ± 1.33 × 104 mol/km2/a, compared with 9.5 ± 6.7 × 105 mol/km2/a for alkalinity and 8.8 ± 6.2 × 105 mol/km2/a for DIC. To compare with literature data, yields for the major estuary across the Taiwan Strait (Jiulong River) are comparable except for P which is extremely low. Primary production supported by these nutrient outflows is insufficient to compensate the DIC supplied by the SGD. As a result, the SGD helps making the coastal waters in Taiwan and Jiulong River heterotrophic.
Biological and epidemiological evidence of anti-allergic effects of traditional Japanese food ume (Prunus mume)
Authors: Kono Ryohei , Nakamura Misa , Nomura Sachiko , Kitano Naomi , Kagiya Tomoko , Okuno Yoshiharu , Inada Ken-ichi , Tokuda Akihiko , Utsunomiya Hirotoshi , Ueno Masami 
Published: July 2018

AbstractJapanese apricot (Prunus mume;ume) is a traditional food in Japan that has been shown to have various beneficial health effects. There is some evidence to suggest thatumeis also effective against allergic disease. Here, we conducted a cross-sectional epidemiological pilot study to examine the association betweenumeintake frequency and allergic symptoms including rhinitis in 563 adults (288 men and 275 women) who resided in Wakayama, Japan. After adjusting for age, present illness and medication, women with highumeintake had significantly lower odds ratio (OR) for the presence of symptoms of allergy [OR: 0.49 with 95% confidence interval (CI): 0.25–0.97]. Therefore, we investigated the anti-allergic effect ofumeon passive cutaneous anaphylaxis (PCA) reaction in immunoglobulin E (IgE)-sensitized mice. The animal study demonstrated that oral administration ofumeextract attenuated the PCA reaction and mast cell degranulation. Furthermore, RBL-2H3 mast cells were used to identify anti-allergicumecompounds. The followingumecompounds inhibited IgE-mediated mast cell degranulation: vanillin, syringic acid, protocatechuic aldehyde, lyoniresinol andp-coumaric acid. These results suggested thatumehas the potential to inhibit mast cell degranulation and may be associated with reduced risk of allergic symptoms in women.