bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems
Authors: Caputi Luigi , Carradec Quentin , Eveillard Damien , Kirilovsky Amos , Pelletier Eric , Pierella Karlusich Juan J. , Rocha Jimenez Vieira Fabio , Villar Emilie , Chaffron Samuel , Malviya Shruti , Scalco Eleonora , Acinas Silvia G. , Alberti Adriana , Aury Jean‐Marc , Benoiston Anne‐Sophie , Bertrand Alexis , Biard Tristan , Bittner Lucie , Boccara Martine , Brum Jennifer R. , Brunet Christophe , Busseni Greta , Carratalà Anna , Claustre Hervé , Coelho Luis Pedro , Colin Sébastien , D'Aniello Salvatore , Da Silva Corinne , Del Core Marianna , Doré Hugo , Gasparini Stéphane , Kokoszka Florian , Jamet Jean‐Louis , Lejeusne Christophe , Lepoivre Cyrille , Lescot Magali , Lima‐Mendez Gipsi , Lombard Fabien , Lukeš Julius , Maillet Nicolas , Madoui Mohammed‐Amin , Martinez Elodie , Mazzocchi Maria Grazia , Néou Mario B. , Paz‐Yepes Javier , Poulain Julie , Ramondenc Simon , Romagnan Jean‐Baptiste , Roux Simon , Salvagio Manta Daniela , Sanges Remo , Speich Sabrina , Sprovieri Mario , Sunagawa Shinichi , Taillandier Vincent , Tanaka Atsuko , Tirichine Leila , Trottier Camille , Uitz Julia , Veluchamy Alaguraj , Veselá Jana , Vincent Flora , Yau Sheree , Kandels‐Lewis Stefanie , Searson Sarah , Dimier Céline , Picheral Marc ,   Tara Oceans Coordinators, Bork Peer , Boss Emmanuel , de Vargas Colomban , Follows Michael J. , Grimsley Nigel , Guidi Lionel , Hingamp Pascal , Karsenti Eric , Sordino Paolo , Stemmann Lars , Sullivan Matthew B. , Tagliabue Alessandro , Zingone Adriana , Garczarek Laurence , d'Ortenzio Fabrizio , Testor Pierre , Not Fabrice , d'Alcalà Maurizio Ribera , Wincker Patrick , Bowler Chris , Iudicone Daniele 
Published: January 2019

AbstractPredicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio‐oceanographic and bio‐omics data sets fromTaraOceans in the context of the iron products from two state‐of‐the‐art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large‐scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.
Geology and Fluid Discharge at Dorado Outcrop, a Low Temperature Ridge‐Flank Hydrothermal System
Authors: Wheat C. Geoffrey , Hartwell Anne M. , McManus James , Fisher Andrew T. , Orcutt Beth N. , Schlicht Lucy E. M. , Niedenzu Sara , Bach Wolfgang 
Published: January 2019

AbstractTwo expeditions to Dorado Outcrop on the eastern flank of the East Pacific Rise and west of the Middle America Trench collected images, video, rocks, and sediment samples and measured temperature and fluid discharge rates to document the physical and biogeochemical characteristics of a regional, low‐temperature (~15 °C) hydrothermal system. Analysis of video and images identified lava morphologies: pillow, lobate, and sheet flows. Glasses from collected lavas were consistent with an off‐axis formation. Hydrothermal discharge generally occurs through pillow lavas but is patchy, sporadic, and sometimes ceases at particular sites of discharge. Yearlong temperature measurements at five of these discharge sites show daily ranges that oscillate with tidal frequencies by 6 °C or more. Instantaneous fluid discharge rates (0.16 to 0.19 L/s) were determined resulting in a calculated discharge of ~200 L/s when integrated over the area defined by the most robust fluid discharge. Such discharge has a power output of 10–12 MW. Hydrothermal seepage through thin sediment adjacent to the outcrop accounts for <3% of this discharge, but seepage may support an oxic sediment column. High extractable Mn concentrations and depleted δ13C in the low but variable organic solid phase suggest that hydrothermal fluids provide a source for manganese accumulation and likely enhance the oxidation of organic carbon. Comparisons of the physical and geochemical characteristics at Dorado and Baby Bare Outcrops, the latter being the only other site of ridge‐flank hydrothermal discharge that has been sampled directly, suggest commonalities and differences that have implications for future discoveries.
D‐Region High‐Latitude Forcing Factors
Authors: Macotela Edith L. , Clilverd Mark , Manninen Jyrki , Moffat‐Griffin Tracy , Newnham David A. , Raita Tero , Rodger Craig J. 
Published: January 2019

AbstractThe subionospheric very low frequency (VLF) radio wave technique provides the possibility of investigating the response of the ionospheric D‐region to a diversity of transient and long‐term physical phenomena originating from above (e.g., energetic particle precipitation) and from below (e.g., atmospheric waves). In this study, we identify the periodicities that appear in VLF measurements and investigate how they may be related to changes in space weather and atmospheric activity. The powerful VLF signal transmitted from NAA (24 kHz) on the east coast of the United States, and received at Sodankylä, Finland, was analyzed. Wavelet transform, wavelet power spectrum, wavelet coherence, and cross‐wavelet spectrum were computed for daily averages of selected ionospheric, space weather, and atmospheric parameters from November 2008 until June 2018. Our results show that the significant VLF periods that appear during solar cycle 24 are the annual oscillation, semiannual oscillation, 121‐day, 86‐day, 61‐day, and solar rotation oscillations. We found that the annual oscillation corresponds to variability in mesospheric temperature and solar Lyman‐α (Ly‐α) flux and the semiannual oscillation to variability in space weather‐related parameters. The solar rotation oscillation observed in the VLF variability is mainly related to the Ly‐α flux variation at solar maximum and to geomagnetic activity variation during the declining phase of the solar cycle. Our results are important since they strengthen our understanding of the Earth's D‐region response to solar and atmospheric forcing.
Strain Localization and Weakening Processes in Viscously Deforming Rocks: Numerical Modeling Based on Laboratory Torsion Experiments
Authors: Döhmann M. J. E. A. , Brune S. , Nardini L. , Rybacki E. , Dresen G. 
Published: January 2019

AbstractLocalization processes in the viscous lower crust generate ductile shear zones over a broad range of scales affecting long‐term lithosphere deformation and the mechanical response of faults during the seismic cycle. Here we use centimeter‐scale numerical models in order to gain detailed insight into the processes involved in strain localization and rheological weakening in viscously deforming rocks. Our 2‐D Cartesian models are benchmarked to high‐temperature and high‐pressure torsion experiments on Carrara marble samples containing a single weak Solnhofen limestone inclusion. The models successfully reproduce bulk stress‐strain transients and final strain distributions observed in the experiments by applying a simple, first‐order softening law that mimics rheological weakening. We find that local stress concentrations forming at the inclusion tips initiate strain localization inside the host matrix. At the tip of the propagating shear zone, weakening occurs within a process zone, which expands with time from the inclusion tips toward the matrix. Rheological weakening is a precondition for shear zone localization, and the width of this shear zone is found to be controlled by the degree of softening. Introducing a second softening step at elevated strain, a high strain layer develops inside the localized shear zone, analogous to the formation of ultramylonite bands in mylonites. These results elucidate the transient evolution of stress and strain rate during inception and maturation of ductile shear zones.
Inadvertent Localized Intensification of Precipitation by Aircraft
Authors: Moisseev Dmitri , Lautaportti Susanna , Alku Laura , Tabakova Ksenia , O'Connor Ewan J. , Leskinen Matti , Kulmala Markku 
Published: January 2019

AbstractEleven years of dual‐polarization weather radar data, complemented by satellite and lidar observations, were used to investigate the origin of areas of localized intensification of precipitation spotted in the vicinity of Helsinki‐Vantaa airport. It was observed that existing precipitation is enhanced locally on spatial scales from a few kilometers to several tens of kilometers. The precipitation intensity in these localized areas was 6–14 times higher than the background large‐scale precipitation rate. Surface observations and dual‐polarization radar data indicate that snowflakes within the ice portion of the falling precipitation in the intensification regions are larger and more isotropic than in the surrounding precipitation. There appears to be an increase in the ice particle number concentration within the intensification region. The observed events were linked to arriving or departing air traffic. We advocate that the mechanism responsible for intensification is aircraft‐produced ice particles boosting the aggregation growth of snowflakes.
Formation of Central Pits in Impact Craters on Mars: A Statistical Investigation of Proposed Mechanisms
Authors: Peel Samantha E. , Burr Devon M. , Tran Liem 
Published: January 2019

AbstractCentral pit craters (CPCs) are complex craters that exhibit depressions within their floors or central uplifts. Some proposed models for central pit formation can be grouped by similar mechanism: (A) explosive volatile release, (B) central peak collapse, and (C) drainage of subsurface melted volatiles. We test these groups of mechanisms for central pit formation on Mars based on morphometries expected from each mechanism. Volatiles in the target (A and C) would be expected to result in a correlation with layered ejecta, also formed from volatiles, for CPCs over non‐CPCs. Central peak collapse (B) should result in larger diameters for pit rims than central peaks due to outward flow. Explosive volatile release (A) should yield smaller volumes for pit rims than pits due to mass loss. Data were collected on Context Camera images and digital elevation models for random samples of CPCs to assess the presence of these expected morphologies. Results of a Fisher exact test showed no preference in layered ejecta with CPCs over non‐CPCs, inconsistent with volatiles in the target. Results of an independent t test showed that central pit rim diameters are larger than central peak diameters, supporting some component of central peak collapse, although measurement uncertainty makes this interpretation tentative. Central pit rim volumes were not found to be statistically smaller than their pits, weighing against formation by explosive volatile release. Thus, our findings do not support any single group of formation mechanism tested here, although they allow for formation by some combination of these (or other) processes.
Formation of Complex Craters in Layered Targets With Material Anisotropy
Authors: Hopkins Ryan T. , Osinski Gordon R. , Collins Gareth S. 
Published: January 2019

AbstractMeteorite impacts often occur in layered targets, where the strength of the target varies as a function of depth, but this complexity is often not represented in numerical impact simulations because of the high computational cost of resolving thin layers. To address this limitation, we developed a method to approximate the effect of multiple thin weak layers within a sedimentary sequence using a single material layer to represent the entire sequence. Our approach, implemented in the iSALE (impact‐Simplified Arbitrary Lagrangian Eulerian) shock physics code, combines an anisotropic yield criterion with a cell‐based method to track the orientation of layers. To demonstrate the efficacy of the method and constrain parameters of the anisotropic strength model required to replicate the effects of thin, weak layers, we compare results of simulations of an ~20‐ to 25‐km diameter complex crater on Earth using the new method to those from simulations that explicitly resolve multiple thin weak layers. We show that our approach allows for a reduction in computational cost, negating the need for an increase in spatial resolution to resolve thin layers in the target, while replicating crater formation and final morphology from the high‐resolution models. In keeping with field observations, we also find that anisotropic layers may be responsible for a lack of central uplift expression observed at many craters formed in targets with thick sedimentary layers (e.g., the Haughton and Ries impact structures).
RETRACTED ARTICLE: Rifaximin alters gut microbiota profile, but does not affect systemic inflammation - a randomized controlled trial in common variable immunodeficiency
Authors: Jørgensen S. F. , Macpherson M. E. , Bjørnetrø T. , Holm K. , Kummen M. , Rashidi A. , Michelsen A. E. , Lekva T. , Halvorsen B. , Trøseid M. , Mollnes T. E. , Berge R. K. , Yndestad A. , Ueland T. , Karlsen T. H. , Aukrust P. , Hov J. R. , Fevang B. 
Published: January 2019

AbstractCommon variable immunodeficiency (CVID) patients have reduced gut microbial diversity compared to healthy controls. The reduced diversity is associated with gut leakage, increased systemic inflammation and ten “key” bacteria that capture the gut dysbiosis (dysbiosis index) in CVID. Rifaximin is a broad-spectrum non-absorbable antibiotic known to reduce gut leakage (lipopolysaccharides, LPS) in liver disease. In this study, we explored as a ‘proof of concept’ that altering gut microbial composition could reduce systemic inflammation, using CVID as a disease model. Forty adult CVID patients were randomized, (1:1) to twice-daily oral rifaximin 550 mg versus no treatment for 2 weeks in an open-label, single-centre study. Primary endpoints were reduction in plasma/serum levels of soluble (s) CD14, sCD25, sCD163, neopterin, CRP, TNF, LPS and selected cytokines measured at 0, 2 and 8 weeks. Secondary endpoint was changes in intra-individual bacterial diversity in stool samples. Rifaximin-use did not significantly change any of the inflammation or gut leakage markers, but decreased gut microbial diversity compared with no treatment (p = 0.002). Importantly, the gut bacteria in the CVID dysbiosis index were not changed by rifaximin. The results suggest that modulating gut microbiota by rifaximin is not the chosen intervention to affect systemic inflammation, at least not in CVID.
Royal jelly peptides: potential inhibitors of β-secretase in N2a/APP695swe cells
Authors: Zhang Xueqing , Yu Yi , Sun Ping , Fan Zhen , Zhang Wensheng , Feng Chengqiang 
Published: January 2019

AbstractRoyal jelly (RJ) is a type of natural health product with a long history of use. Royal jelly peptides (RJPs) obtained from RJ have numerous bioactivities. To study the neuroprotective effect of RJPs, major royal jelly proteins were digested into crude RJPs and subsequently purified by RP-HPLC. Purified RJP fractions were evaluated in N2a/APP695swe cells. Our results indicated that purified royal jelly peptides (RJPs) (1–9 μg/mL) could inhibit external beta-amyloid 40 (Aβ1-40) and beta-amyloid 42 (Aβ1-42) production through the down-regulation of β-secretase (BACE1) in N2a/APP695 cells. The modulation of BACE1 may be related to histone acetylation modification. Our results demonstrated a neuroprotective function of RJPs, which indicates that RJPs may serve as potential β-secretase inhibitors in ameliorating Aβ-related pathology in Alzheimer’s Disease.
Central place foragers select ocean surface convergent features despite differing foraging strategies
Authors: Oliver Matthew J. , Kohut Josh T. , Bernard Kim , Fraser William , Winsor Peter , Statscewich Hank , Fredj Erick , Cimino Megan , Patterson-Fraser Donna , Carvalho Filipa 
Published: January 2019

AbstractDiscovering the predictors of foraging locations can be challenging, and is often the critical missing piece for interpreting the ecological significance of observed movement patterns of predators. This is especially true in dynamic coastal marine systems, where planktonic food resources are diffuse and must be either physically or biologically concentrated to support upper trophic levels. In the Western Antarctic Peninsula, recent climate change has created new foraging sympatry between Adélie (Pygoscelis adeliae) and gentoo (P. papua) penguins in a known biological hotspot near Palmer Deep canyon. We used this recent sympatry as an opportunity to investigate how dynamic local oceanographic features affect aspects of the foraging ecology of these two species. Simulated particle trajectories from measured surface currents were used to investigate the co-occurrence of convergent ocean features and penguin foraging locations. Adélie penguin diving activity was restricted to the upper mixed layer, while gentoo penguins often foraged much deeper than the mixed layer, suggesting that Adélie penguins may be more responsive to dynamic surface convergent features compared to gentoo penguins. We found that, despite large differences in diving and foraging behavior, both shallow-diving Adélie and deeper-diving gentoo penguins strongly selected for surface convergent features. Furthermore, there was no difference in selectivity for shallow- versus deep-diving gentoo penguins. Our results suggest that these two mesopredators are selecting surface convergent features, however, how these surface signals are related to subsurface prey fields is unknown.
Windshield wipers on connected vehicles produce high-accuracy rainfall maps
Authors: Bartos Matthew , Park Hyongju , Zhou Tian , Kerkez Branko , Vasudevan Ramanarayan 
Published: January 2019

AbstractConnected vehicles are poised to transform the field of environmental sensing by enabling acquisition of scientific data at unprecedented scales. Drawing on a real-world dataset collected from almost 70 connected vehicles, this study generates improved rainfall estimates by combining weather radar with windshield wiper observations. Existing methods for measuring precipitation are subject to spatial and temporal uncertainties that compromise high-precision applications like flash flood forecasting. Windshield wiper measurements from connected vehicles correct these uncertainties by providing precise information about the timing and location of rainfall. Using co-located vehicle dashboard camera footage, we find that wiper measurements are a stronger predictor of binary rainfall state than traditional stationary gages or radar-based measurements. We introduce a Bayesian filtering framework that generates improved rainfall estimates by updating radar rainfall fields with windshield wiper observations. We find that the resulting rainfall field estimate captures rainfall events that would otherwise be missed by conventional measurements. We discuss how these enhanced rainfall maps can be used to improve flood warnings and facilitate real-time operation of stormwater infrastructure.
PD-1/PD-L1 Pathway Modulates Macrophage Susceptibility to Mycobacterium tuberculosis Specific CD8+ T cell Induced Death
Authors: Suarez Guadalupe Verónica , Melucci Ganzarain Claudia del Carmen , Vecchione María Belén , Trifone César Ariel , Marín Franco José Luis , Genoula Melanie , Moraña Eduardo José , Balboa Luciana , Quiroga Maria Florencia 
Published: January 2019

AbstractCD8+T cells contribute to tuberculosis (TB) infection control by inducing death of infected macrophages. Mycobacterium tuberculosis (Mtb) infection is associated with increased PD-1/PD-L1 expression and alternative activation of macrophages. We aimed to study the role of PD-1 pathway and macrophage polarization on Mtb-specific CD8+T cell-induced macrophage death. We observed that both PD-L1 on CD14+ cells and PD-1 on CD8+T cells were highly expressed at the site of infection in pleurisy TB patients’ effusion samples (PEMC). Moreover, a significant increase in CD8+T cells’ Mtb-specific degranulation from TB-PEMC vs. TB-PBMC was observed, which correlated with PD-1 and PDL-1 expression. In an in vitro model, M1 macrophages were more susceptible to Mtb-specific CD8+T cells’ cytotoxicity compared to M2a macrophages and involved the transfer of cytolytic effector molecules from CD8+T lymphocytes to target cells. Additionally, PD-L1 blocking significantly increased the in vitro Ag-specific CD8+T cell cytotoxicity against IFN-γ-activated macrophages but had no effect over cytotoxicity on IL-4 or IL-10-activated macrophages. Interestingly, PD-L1 blocking enhanced Mtb-specific CD8+ T cell killing of CD14+ cells from human tuberculous pleural effusion samples. Our data indicate that PD-1/PD-L1 pathway modulates antigen-specific cytotoxicity against M1 targets in-vitro and encourage the exploration of checkpoint blockade as new adjuvant for TB therapies.
A novel tankyrase inhibitor, MSC2504877, enhances the effects of clinical CDK4/6 inhibitors
Authors: Menon Malini , Elliott Richard , Bowers Leandra , Balan Nicolae , Rafiq Rumana , Costa-Cabral Sara , Munkonge Felix , Trinidade Ines , Porter Roderick , Campbell Andrew D. , Johnson Emma R. , Esdar Christina , Buchstaller Hans-Peter , Leuthner Birgitta , Rohdich Felix , Schneider Richard , Sansom Owen , Wienke Dirk , Ashworth Alan , Lord Christopher J. 
Published: January 2019

AbstractInhibition of the PARP superfamily tankyrase enzymes suppresses Wnt/β-catenin signalling in tumour cells. Here, we describe here a novel, drug-like small molecule inhibitor of tankyrase MSC2504877 that inhibits the growth of APC mutant colorectal tumour cells. Parallel siRNA and drug sensitivity screens showed that the clinical CDK4/6 inhibitor palbociclib, causes enhanced sensitivity to MSC2504877. This tankyrase inhibitor-CDK4/6 inhibitor combinatorial effect is not limited to palbociclib and MSC2504877 and is elicited with other CDK4/6 inhibitors and toolbox tankyrase inhibitors. The addition of MSC2504877 to palbociclib enhances G1 cell cycle arrest and cellular senescence in tumour cells. MSC2504877 exposure suppresses the upregulation of Cyclin D2 and Cyclin E2 caused by palbociclib and enhances the suppression of phospho-Rb, providing a mechanistic explanation for these effects. The combination of MSC2504877 and palbociclib was also effective in suppressing the cellular hyperproliferative phenotype seen in Apc defective intestinal stem cells in vivo. However, the presence of an oncogenic Kras p.G12D mutation in mice reversed the effects of the MSC2504877/palbociclib combination, suggesting one molecular route that could lead to drug resistance.