bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitroelucidation of suppression effects of composts to soil-borne pathogenPhytophthora nicotianaeon pepper plants using 16S amplicon sequencing and metaproteomics
Authors: Ros Margarita , Blaya Josefa , Baldrian Petr , Bastida Felipe , Richnow Hans H , Jehmlich Nico , Pascual Jose Antonio 
Published: September 2018

AbstractCompost production is a critical component of organic waste management. One of the most important properties of compost is its ability to suppress soil-borne pathogens such asPhytophthora nicotianaein pepper plants. Both the physico-chemical and biological properties of composts can be responsible for the suppression of pathogens, although biological properties are the main driver. In this study, we analyzed composts with various levels of suppressiveness againstP. nicotianae. We analyzed both physico-chemical properties like pH and electrical conductivity and biological properties like microbial activity, amplicon sequencing and metaproteomics. We believed that the link between community structures and proteins could provide deep insights into the mechanism of compost suppressiveness. Our results indicate that there are differences between suppressive and non-suppressive composts at the phylogenetic level (sequencing) and at the functional level (based on analysis of the cluster of orthologous groups, COGs). The proteins identified were assigned to the carbohydrate process, cell wall structure and inorganic ion transport and metabolism.Proteobacteriacould also be new indicators ofP. nicotianaesuppression.
Vertical Propagation of Middepth Zonal Currents Associated With Surface Wind Forcing in the Equatorial Indian Ocean
Authors: Huang Ke , McPhaden Michael J. , Wang Dongxiao , Wang Weiqiang , Xie Qiang , Chen Ju , Shu Yeqiang , Wang Qiang , Li Jian , Yao Jinglong 
Published: September 2018

AbstractThe vertical propagation of middepth (200–1,500 m) zonal velocity in the equatorial Indian Ocean (EIO) and its relationship with surface wind forcing are investigated. We focus on semiannual time scales, using in situ mooring observations and an oceanic reanalysis product that can reasonably well reproduce the structure and magnitude of the observed middepth zonal velocity in the EIO. The pronounced semiannual cycle in observed middepth zonal currents indicates a clear upward phase propagation with particularly robust signatures at depths of 500–1,000 m between 3°S to 3°N, 70 to 85°E. The main characteristics of the middepth currents are consistent with vertically propagating first‐meridional‐mode Rossby wave at semiannual period. Theory suggests that equatorial Kelvin waves, forced by zonal wind variations in the western half of the basin, transfer energy downward and eastward, reflecting into Rossby waves at the eastern boundary. These reflected Rossby waves transfer energy downward and westward, contributing greatly to observed phase propagation at middepths in the EIO.
Ocean Stratification and Low Melt Rates at the Ross Ice Shelf Grounding Zone
Authors: Begeman Carolyn Branecky , Tulaczyk Slawek M. , Marsh Oliver J. , Mikucki Jill A. , Stanton Timothy P. , Hodson Timothy O. , Siegfried Matthew R. , Powell Ross D. , Christianson Knut , King Matt A. 
Published: September 2018

AbstractOcean‐driven melting of ice shelves is a primary mechanism for ice loss from Antarctica. However, due to the difficulty in accessing the sub‐ice shelf ocean cavity, the relationship between ice shelf melting and ocean conditions is poorly understood, particularly near the grounding zone, where the ice transitions from grounded to floating. We present the first borehole oceanographic observations from the grounding zone of the Ross Ice Shelf, Antarctica's largest ice shelf by area. Contrary to predictions that tidal currents near grounding zones mix the water column, we found that Ross Ice Shelf waters were vertically stratified. Current velocities at middepth in the ocean cavity did not change significantly over measurement periods at two different parts of the tidal cycle. The observed stratification resulted in low melt rates near this portion of the grounding zone, inferred from phase‐sensitive radar observations. These melt rates were generally <10 cm/year, which is lower than average for the Ross Ice Shelf (~20 cm/year). Melt rates may be higher at portions of the grounding zone that experience higher subglacial discharge or stronger tidal mixing. Stratification in the cavity at the borehole site was prone to diffusive convection as a result of ice shelf melting. Since diffusive convection influences vertical heat and salt fluxes differently than shear‐driven turbulence, this process may affect ice shelf melting and merits further consideration in ocean models of sub‐ice shelf circulation.
On the Statistical Significance of Climatic Trends Estimated From GPS Tropospheric Time Series
Authors: Alshawaf F. , Zus F. , Balidakis K. , Deng Z. , Hoseini M. , Dick G. , Wickert J. 
Published: September 2018

AbstractFor more than two decades, Global Positioning System (GPS) tropospheric delays have successfully been exploited to monitor the tropospheric water vapor in near real time and reprocessing mode. Although reprocessed data are considered reliable for climatic research, it is important to address the often present gaps, inhomogeneities, and to use a proper model to describe the stochastic part of the time series so that trustworthy trends are estimated. Having relatively long time series, daily reprocessed tropospheric Zenith Total Delay, precipitable water vapor (PWV), and gradients from the Tide Gauge benchmark monitoring network are used in this work to estimate climatic trends. We use a first‐order autoregressive model AR(1) to describe the residuals after the trend estimation so that a correct trend uncertainty is estimated. Using the same model, we obtain the number of years of PWV data required to estimate statistically significant trends. For comparison, we produce tropospheric parameters at each Tide Gauge station based on ERA‐Interim refractivity fields. We found that 83% of 64 GPS stations show a positive PWV trend below 1 mm/decade independent of the time interval, with approximately half of the trends indicated significant. There is a strong correlation (86%) between the Global Navigation Satellite Systems and ERA‐Interim PWV trends. The trends tend to increase when moving east and south on the European map. The results show a percentage change of PWV of 3–8% per a degree Celsius rise in temperature. The number of years required to detect significant PWV trends varies between 30 and 40 years.
Response of Tropical Terrestrial Gross Primary Production to the Super El Niño Event in 2015
Authors: Zhu Jiawen , Zhang Minghua , Zhang Yao , Zeng Xiaodong , Xiao Xiangming 
Published: September 2018

AbstractThe gross primary production (GPP) in tropical terrestrial ecosystems plays a critical role in the global carbon cycle and climate change. The strong 2015–2016 El Niño event offers a unique opportunity to investigate how GPP in the tropical terrestrial ecosystems responds to climatic forcing. This study uses two GPP products and concurrent climate data to investigate the GPP anomalies and their underlying causes. We find that both GPP products show an enhanced GPP in 2015 for the tropical terrestrial ecosystem as a whole relative to the multiyear mean of 2001–2015, and this enhancement is the net result of GPP increase in tropical forests and decrease in nonforests. We show that the increased GPP in tropical forests during the El Nino event is consistent with increased photosynthesis active radiation as a result of a reduction in clouds, while the decreased GPP in nonforests is consistent with increased water stress as a result of a reduction of precipitation and an increase of temperature. These results reveal the strong coupling of ecosystem and climate that is different in forest and nonforest ecosystems and provide a test case for carbon cycle parameterization and carbon‐climate feedback simulation in models.
Cervical squamous cell carcinoma-secreted exosomal miR-221-3p promotes lymphangiogenesis and lymphatic metastasis by targeting VASH1
Authors: Zhou Chen-Fei , Ma Jing , Huang Lei , Yi Hong-Yan , Zhang Yan-Mei , Wu Xiang-Guang , Yan Rui-Ming , Liang Li , Zhong Mei , Yu Yan-Hong , Wu Sha , Wang Wei 
Published: September 2018

AbstractCancer-secreted exosomal miRNAs are emerging mediators of cancer-stromal cross-talk in the tumor environment. Our previous miRNAs array of cervical squamous cell carcinoma (CSCC) clinical specimens identified upregulation of miR-221-3p. Here, we show that miR-221-3p is closely correlated with peritumoral lymphangiogenesis and lymph node (LN) metastasis in CSCC. More importantly, miR-221-3p is characteristically enriched in and transferred by CSCC-secreted exosomes into human lymphatic endothelial cells (HLECs) to promote HLECs migration and tube formation in vitro, and facilitate lymphangiogenesis and LN metastasis in vivo according to both gain-of-function and loss-of-function experiments. Furthermore, we identify vasohibin-1 (VASH1) as a novel direct target of miR-221-3p through bioinformatic target prediction and luciferase reporter assay. Re-expression and knockdown of VASH1 could respectively rescue and simulate the effects induced by exosomal miR-221-3p. Importantly, the miR-221-3p-VASH1 axis activates the ERK/AKT pathway in HLECs independent of VEGF-C. Finally, circulating exosomal miR-221-3p levels also have biological function in promoting HLECs sprouting in vitro and are closely associated with tumor miR-221-3p expression, lymphatic VASH1 expression, lymphangiogenesis, and LN metastasis in CSCC patients. In conclusion, CSCC-secreted exosomal miR-221-3p transfers into HLECs to promote lymphangiogenesis and lymphatic metastasis via downregulation of VASH1 and may represent a novel diagnostic biomarker and therapeutic target for metastatic CSCC patients in early stages.
Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations
Authors: Lambert Stefan , Tragin Margot , Lozano Jean-Claude , Ghiglione Jean-François , Vaulot Daniel , Bouget François-Yves , Galand Pierre E 
Published: September 2018

Abstract
Seasonality in marine microorganisms has been classically observed in phytoplankton blooms, and more recently studied at the community level in prokaryotes, but rarely investigated at the scale of individual microbial taxa. Here we test if specific marine eukaryotic phytoplankton, bacterial and archaeal taxa display yearly rhythms at a coastal site impacted by irregular environmental perturbations. Our seven-year study in the Bay of Banyuls (North Western Mediterranean Sea) shows that despite some fluctuating environmental conditions, many microbial taxa displayed significant yearly rhythms. The robust rhythmicity was found in both autotrophs (picoeukaryotes and cyanobacteria) and heterotrophic prokaryotes. Sporadic meteorological events and irregular nutrient supplies did, however, trigger the appearance of less common non-rhythmic taxa. Among the environmental parameters that were measured, the main drivers of rhythmicity were temperature and day length. Seasonal autotrophs may thus be setting the pace for rhythmic heterotrophs. Similar environmental niches may be driving seasonality as well. The observed strong association between Micromonas and SAR11, which both need thiamine precursors for growth, could be a first indication that shared nutritional niches may explain some rhythmic patterns of co-occurrence.
Niche and fitness differences determine invasion success and impact in laboratory bacterial communities
Authors: Li Shao-peng , Tan Jiaqi , Yang Xian , Ma Chao , Jiang Lin 
Published: September 2018

Abstract
There is increasing awareness of invasion in microbial communities worldwide, but the mechanisms behind microbial invasions remain poorly understood. Specifically, we know little about how the evolutionary and ecological differences between invaders and natives regulate invasion success and impact. Darwin’s naturalization hypothesis suggests that the phylogenetic distance between invaders and natives could be a useful predictor of invasion, and modern coexistence theory proposes that invader-native niche and fitness differences combine to determine invasion outcome. However, the relative importance of phylogenetic distance, niche difference and fitness difference for microbial invasions has rarely been examined. By using laboratory bacterial microcosms as model systems, we experimentally assessed the roles of these differences for the success of bacterial invaders and their impact on native bacterial community structure. We found that the phylogenetic distance between invaders and natives failed to explain invasion success and impact for two of three invaders at the phylogenetic scale considered. Further, we found that invasion success was better explained by invader-native niche differences than relative fitness differences for all three invaders, whereas invasion impact was better explained by invader-native relative fitness differences than niche differences. These findings highlight the utility of considering modern coexistence theory to gain a more mechanistic understanding of microbial invasions.
Silencing of TGFβ signalling in microglia results in impaired homeostasis
Authors: Zöller Tanja , Schneider Artur , Kleimeyer Christian , Masuda Takahiro , Potru Phani Sankar , Pfeifer Dietmar , Blank Thomas , Prinz Marco , Spittau Björn 
Published: September 2018

AbstractTGFβ1 has been implicated in regulating functional aspects of several distinct immune cell populations including central nervous system (CNS) resident microglia. Activation and priming of microglia have been demonstrated to contribute to the progression of neurodegenerative diseases and, thus, underlie stringent control by endogenous regulatory factors including TGFβ1. Here, we demonstrate that deletion of Tgfbr2 in adult postnatal microglia does neither result in impairment of the microglia-specific gene expression signatures, nor is microglial survival and maintenance affected. Tgfbr2-deficient microglia were characterised by distinct morphological changes and transcriptome analysis using RNAseq revealed that loss of TGFβ signalling results in upregulation of microglia activation and priming markers. Moreover, protein arrays demonstrated increased secretion of CXCL10 and CCL2 accompanied by activation of immune cell signalling as evidenced by increased phosphorylation of TAK1. Together, these data underline the importance of microglial TGFβ signalling to regulate microglia adaptive changes.
LISA improves statistical analysis for fMRI
Authors: Lohmann Gabriele , Stelzer Johannes , Lacosse Eric , Kumar Vinod J. , Mueller Karsten , Kuehn Esther , Grodd Wolfgang , Scheffler Klaus 
Published: September 2018

AbstractOne of the principal goals in functional magnetic resonance imaging (fMRI) is the detection of local activation in the human brain. However, lack of statistical power and inflated false positive rates have recently been identified as major problems in this regard. Here, we propose a non-parametric and threshold-free framework called LISA to address this demand. It uses a non-linear filter for incorporating spatial context without sacrificing spatial precision. Multiple comparison correction is achieved by controlling the false discovery rate in the filtered maps. Compared to widely used other methods, it shows a boost in statistical power and allows to find small activation areas that have previously evaded detection. The spatial sensitivity of LISA makes it especially suitable for the analysis of high-resolution fMRI data acquired at ultrahigh field (≥7 Tesla).
Femtosecond photoexcitation dynamics inside a quantum solvent
Authors: Thaler Bernhard , Ranftl Sascha , Heim Pascal , Cesnik Stefan , Treiber Leonhard , Meyer Ralf , Hauser Andreas W. , Ernst Wolfgang E. , Koch Markus 
Published: September 2018

AbstractThe observation of chemical reactions on the time scale of the motion of electrons and nuclei has been made possible by lasers with ever shortened pulse lengths. Superfluid helium represents a special solvent that permits the synthesis of novel classes of molecules that have eluded dynamical studies so far. However, photoexcitation inside this quantum solvent triggers a pronounced response of the solvation shell, which is not well understood. Here, we present a mechanistic description of the solvent response to photoexcitation of indium (In) dopant atoms inside helium nanodroplets (HeN), obtained from femtosecond pump–probe spectroscopy and time-dependent density functional theory simulations. For the In–HeN system, part of the excited state electronic energy leads to expansion of the solvation shell within 600 fs, initiating a collective shell oscillation with a period of about 30 ps. These coupled electronic and nuclear dynamics will be superimposed on intrinsic photoinduced processes of molecular systems inside helium droplets.
Regulatory control of DNA end resection by Sae2 phosphorylation
Authors: Cannavo Elda , Johnson Dominic , Andres Sara N. , Kissling Vera M. , Reinert Julia K. , Garcia Valerie , Erie Dorothy A. , Hess Daniel , Thomä Nicolas H. , Enchev Radoslav I. , Peter Matthias , Williams R. Scott , Neale Matt J. , Cejka Petr 
Published: September 2018

AbstractDNA end resection plays a critical function in DNA double-strand break repair pathway choice. Resected DNA ends are refractory to end-joining mechanisms and are instead channeled to homology-directed repair. Using biochemical, genetic, and imaging methods, we show that phosphorylation of Saccharomyces cerevisiae Sae2 controls its capacity to promote the Mre11-Rad50-Xrs2 (MRX) nuclease to initiate resection of blocked DNA ends by at least two distinct mechanisms. First, DNA damage and cell cycle-dependent phosphorylation leads to Sae2 tetramerization. Second, and independently, phosphorylation of the conserved C-terminal domain of Sae2 is a prerequisite for its physical interaction with Rad50, which is also crucial to promote the MRX endonuclease. The lack of this interaction explains the phenotype of rad50S mutants defective in the processing of Spo11-bound DNA ends during meiotic recombination. Our results define how phosphorylation controls the initiation of DNA end resection and therefore the choice between the key DNA double-strand break repair mechanisms.
Digital coding of mechanical stress in a dynamic covalent shape memory polymer network
Authors: Zhang Guogao , Peng Wenjun , Wu Jingjun , Zhao Qian , Xie Tao 
Published: September 2018

AbstractControlling stresses in materials presents many unusual opportunities for their engineering applications. The potential for current approaches is severely limited by the intrinsic tie between the stress and the geometric shape. Here, we report a material concept that allows stress management in a highly efficient digital manner while decoupling the stress and the geometric shape. This is realized in a dynamic covalent shape memory polymer network, for which the elastic shape memory sets the baseline stress level and maintains the geometric shape while the plasticity enabled by the dynamic bond exchange allows stress tuning. With a digital gray scale photothermal mechanism, any arbitrarily defined stress distribution can be created in a free-standing polymer film. The naturally invisible stresses can be further visualized as mechanical colors under polarized light, revealing its potential for encoding hidden information. Our approach expands the technological potential in many areas for which stresses are relevant.
Coupled microbial bloom and oxygenation decline recorded by magnetofossils during the Palaeocene–Eocene Thermal Maximum
Authors: Chang Liao , Harrison Richard J. , Zeng Fan , Berndt Thomas A. , Roberts Andrew P. , Heslop David , Zhao Xiang 
Published: September 2018

AbstractUnderstanding marine environmental change and associated biological turnover across the Palaeocene–Eocene Thermal Maximum (PETM; ~56 Ma)—the most pronounced Cenozoic short-term global warming event—is important because of the potential role of the ocean in atmospheric CO2 drawdown, yet proxies for tracing marine productivity and oxygenation across the PETM are limited and results remain controversial. Here we show that a high-resolution record of South Atlantic Ocean bottom water oxygenation can be extracted from exceptionally preserved magnetofossils—the bioinorganic magnetite nanocrystals produced by magnetotactic bacteria (MTB) using a new multiscale environmental magnetic approach. Our results suggest that a transient MTB bloom occurred due to increased nutrient supply. Bottom water oxygenation decreased gradually from the onset to the peak PETM. These observations provide a record of microbial response to the PETM and establish the value of magnetofossils as palaeoenvironmental indicators.
A flow platform for degradation-free CuAAC bioconjugation
Authors: Hatit Marine Z. C. , Reichenbach Linus F. , Tobin John M. , Vilela Filipe , Burley Glenn A. , Watson Allan J. B. 
Published: September 2018

AbstractThe Cu-catalyzed azide-alkyne cycloaddition (CuAAC) reaction is a cornerstone method for the ligation of biomolecules. However, undesired Cu-mediated oxidation and Cu-contamination in bioconjugates limits biomedical utility. Here, we report a generic CuAAC flow platform for the rapid, robust, and broad-spectrum formation of discrete triazole bioconjugates. This process leverages an engineering problem to chemical advantage: solvent-mediated Cu pipe erosion generates ppm levels of Cu in situ under laminar flow conditions. This is sufficient to catalyze the CuAAC reaction of small molecule alkynes and azides, fluorophores, marketed drug molecules, peptides, DNA, and therapeutic oligonucleotides. This flow approach, not replicated in batch, operates at ambient temperature and pressure, requires short residence times, avoids oxidation of sensitive functional groups, and produces products with very low ppm Cu contamination.
Surface degradation mechanisms in precipitation-hardened high-entropy alloys
Authors: Ayyagari Aditya V. , Gwalani Bharat , Muskeri Saideep , Mukherjee Sundeep , Banerjee Rajarshi 
Published: September 2018

AbstractDesign of high-entropy alloys with complex microstructures presents a unique opportunity to combine the best of solid solution strengthening and precipitation hardening. These alloys are potentially disruptive for several high-performance applications including aerospace, oil and gas, nuclear industry, and next-generation tribology. This study presents the thermo-mechanical treatment, microstructural evolution, and surface degradation resistance in precipitation hardenable Al0.3Cu0.3Ti0.2CoCrFeNi high-entropy alloy. The heat-treated alloy consisted of fine precipitates of L12 and L21, strengthening the face-centered cubic solid solution matrix. Potentiodynamic polarization showed nano-galvanic coupling between the intermetallic particles and the matrix. Phase-specific nano-indentation showed that hard intermetallic particles caused three-body wear and higher friction values during sliding wear. The microstructure was correlated with processing conditions and resulting surface degradation resistance using transmission electron microscopy imaging and analysis.