bluuebunny/crossref_metadata_2025 huggingface dataset:
Vertical modeling of the nitrogen cycle in the eastern tropical South Pacific oxygen deficient zone using high‐resolution concentration and isotope measurements
Authors: Peters Brian D. , Babbin Andrew R. , Lettmann Karsten A. , Mordy Calvin W. , Ulloa Osvaldo , Ward Bess B. , Casciotti Karen L.
Published: October 2016

Marine oxygen deficient zones (ODZs) have long been identified as sites of fixed nitrogen (N) loss. However, the mechanisms and rates of N loss have been debated, and traditional methods for measuring these rates are labor‐intensive and may miss hot spots in spatially and temporally variable environments. Here we estimate rates of heterotrophic nitrate reduction, heterotrophic nitrite reduction (denitrification), nitrite oxidation, and anaerobic ammonium oxidation (anammox) at a coastal site in the eastern tropical South Pacific (ETSP) ODZ based on high‐resolution concentration and natural abundance stable isotope measurements of nitrate (NO3−) and nitrite (NO2−). These measurements were used to estimate process rates using a two‐step inverse modeling approach. The modeled rates were sensitive to assumed isotope effects for NO3− reduction and NO2− oxidation. Nevertheless, we addressed two questions surrounding the fates of NO2− in the ODZ: (1) Is NO2− being primarily reduced to N2 or oxidized to NO3− in the ODZ? and (2) what are the contributions of anammox and denitrification to NO2− removal? Depth‐integrated rates from the model suggest that 72–88% of the NO2− produced in the ODZ was oxidized back to NO3−, while 12–28% of NO2− was reduced to N2. Furthermore, our model suggested that 36–74% of NO2− loss was due to anammox, with the remainder due to denitrification. These model results generally agreed with previously measured rates, though with a large range of uncertainty, and they provide a long‐term integrated view that compliments incubation experiments to obtain a broader picture of N cycling in ODZs.
Multidecadal wind‐driven shifts in northwest Pacific temperature, salinity, O2, and PO4
Authors: Kwon Eun Young , Kim Young Ho , Park Young‐Gyu , Park Young‐Hyang , Dunne John , Chang Kyung‐Il
Published: October 2016

The North Pacific gyre boundaries are characterized by stark contrasts in physical and biogeochemical properties. Meridional movement of gyre boundaries, influenced by climate change, can therefore exert a large influence not only on marine ecosystems but also on climate. We examine the evidence for wind‐driven southward shifts in subsurface temperature, salinity, PO4, and O2 within the northwest Pacific from the 1950s to the 2000s. Gyre boundary shifts can explain 30–60% of temperature and salinity trends zonally averaged in the northwest Pacific and observed PO4 and O2 trends along the 137°E and 144°E meridians. The close tie between the wind‐driven shifts in gyre boundaries and the tracer distributions is further supported by results from an eddy‐resolving (0.1° × 0.1°) Geophysical Fluid Dynamics Laboratory climate model, suggesting that the physical and biogeochemical properties averaged within the northwest Pacific gyre boundaries closely follow the latitude changes of the zero Sverdrup stream function with lags of 0 to 3 years. The gyre shift effect on tracer distribution is poorly represented in a coarse resolution (1° × 1°) model due partly to poor representations of fronts and eddies. This study suggests that future changes in northwest Pacific PO4 and O2 content may depend not only on ocean temperature and stratification but also on the ocean gyre response to winds.
An effective approach to evaluate GCM simulated diurnal variation of clouds
Authors: Chen Guoxing , Wang Wei‐Chyung
Published: October 2016

Cloud radiative effects strongly depend on diurnal variations of insolation and cloud radiative properties. In general circulation models (GCMs), even when the daily‐mean cloud properties agree with observations, errors in cloud diurnal cycle can still significantly impact the shortwave radiation and induce model biases. However, this aspect is overlooked in GCM evaluation and intercomparison programs (e.g., Coupled Model Intercomparison Project Phase 5 (CMIP5)), which mainly consider the daily‐mean cloud fraction. This study presents a simple approach of using a diagnostic parameter, the “effective‐daytime cloud fraction” which accounts for the concurrent variation of clouds and insolation, to reveal GCM biases in cloud diurnal variations. The usefulness of the approach is illustrated by the significant biases of cloud diurnal cycle in the Modern‐Era Retrospective analysis for Research and Applications (MERRA) reanalysis when compared with that in the International Satellite Cloud Climatology Project (ISCCP) data. It is thus suggested that the parameter be included as one of the GCM diagnostics for evaluating cloud diurnal cycle in model intercomparisons.
Homogeneity of a global multisatellite soil moisture climate data record
Authors: Su Chun‐Hsu , Ryu Dongryeol , Dorigo Wouter , Zwieback Simon , Gruber Alexander , Albergel Clement , Reichle Rolf H. , Wagner Wolfgang
Published: October 2016

Climate Data Records (CDR) that blend multiple satellite products are invaluable for climate studies, trend analysis and risk assessments. Knowledge of any inhomogeneities in the CDR is therefore critical for making correct inferences. This work proposes a methodology to identify the spatiotemporal extent of the inhomogeneities in a 36 year, global multisatellite soil moisture CDR as the result of changing observing systems. Inhomogeneities are detected at up to 24% of the tested pixels with spatial extent varying with satellite changeover times. Nevertheless, the contiguous periods without inhomogeneities at changeover times are generally longer than 10 years. Although the inhomogeneities have measurable impact on the derived trends, these trends are similar to those observed in ground data and land surface reanalysis, with an average error less than 0.003 m3 m−3 y−1. These results strengthen the basis of using the product for long‐term studies and demonstrate the necessity of homogeneity testing of multisatellite CDRs in general.
Direct space‐based observations of anthropogenic CO2 emission areas from OCO‐2
Authors: Hakkarainen J. , Ialongo I. , Tamminen J.
Published: October 2016

Anthropogenic CO2 emissions from fossil fuel combustion have large impacts on climate. In order to monitor the increasing CO2 concentrations in the atmosphere, accurate spaceborne observations—as available from the Orbiting Carbon Observatory‐2 (OCO‐2)—are needed. This work provides the first direct observation of anthropogenic CO2 from OCO‐2 over the main pollution regions: eastern USA, central Europe, and East Asia. This is achieved by deseasonalizing and detrending OCO‐2 CO2 observations to derive CO2 anomalies. Several small isolated emission areas (such as large cities) are detectable from the anomaly maps. The spatial distribution of the CO2 anomaly matches the features observed in the maps of the Ozone Monitoring Instrument NO2 tropospheric columns, used as an indicator of atmospheric pollution. The results of a cluster analysis confirm the spatial correlation between CO2 and NO2 data over areas with different amounts of pollution. We found positive correlation between CO2 anomalies and emission inventories. The results demonstrate the power of spaceborne data for monitoring anthropogenic CO2 emissions.
Correlating laser‐generated melts with impact‐generated melts: An integrated thermodynamic‐petrologic approach
Authors: Hamann Christopher , Luther Robert , Ebert Matthias , Hecht Lutz , Deutsch Alex , Wünnemann Kai , Schäffer Sebastian , Osterholz Jens , Lexow Bernd
Published: October 2016

Planetary collisions in the solar system typically induce melting and vaporization of the impactor and a certain volume of the target. To study the dynamics of quasi‐instantaneous melting and subsequent quenching under postshock P‐T conditions of impact melting, we used continuous‐wave laser irradiation to melt and vaporize sandstone, iron meteorite, and basalt. Using high‐speed imaging, temperature measurements, and petrologic investigations of the irradiation targets, we show that laser‐generated melts exhibit typical characteristics of impact melts (particularly ballistic ejecta). We then calculate the entropy gains of the laser‐generated melts and compare them with the entropy gains associated with the thermodynamic states produced in hypervelocity impacts at various velocities. In conclusion, our experiments extend currently attainable postshock temperatures in impact experiments to ranges commensurate with impacts in the velocity range of 4–20 km s–1 and allow to study timescales and magnitudes of petrogenetic processes in impact melts.
The tectonic development and erosion of the Knox Subglacial Sedimentary Basin, East Antarctica
Authors: Maritati A. , Aitken A. R. A. , Young D. A. , Roberts J. L. , Blankenship D. D. , Siegert M. J.
Published: October 2016

Sedimentary basins beneath the East Antarctic Ice Sheet (EAIS) have immense potential to inform models of the tectonic evolution of East Antarctica and its ice‐sheet. However, even basic characteristics such as thickness and extent are often unknown. Using airborne geophysical data, we resolve the tectonic architecture of the Knox Subglacial Sedimentary Basin in western Wilkes Land. In addition, we apply an erosion restoration model to reconstruct the original basin geometry for which we resolve geometry typical of a transtensional pull‐apart basin. The tectonic architecture strongly indicates formation as a consequence of the rifting of India from East Gondwana from ca. 160‐130 Ma, and we suggest a spatial link with the western Mentelle Basin offshore Western Australia. The erosion restoration model shows that erosion is confined within the rift margins, suggesting that rift structure has strongly influenced the evolution of the Denman and Scott ice streams.
Saturn's quasiperiodic magnetohydrodynamic waves
Authors: Yates J. N. , Southwood D. J. , Dougherty M. K. , Sulaiman A. H. , Masters A. , Cowley S. W. H. , Kivelson M. G. , Chen C. H. K. , Provan G. , Mitchell D. G. , Hospodarsky G. B. , Achilleos N. , Sorba A. M. , Coates A. J.
Published: October 2016

Quasiperiodic ∼1 h fluctuations have been recently reported by numerous instruments on board the Cassini spacecraft. The interpretation of the sources of these fluctuations has remained elusive to date. Here we provide an explanation for the origin of these fluctuations using magnetometer observations. We find that magnetic field fluctuations at high northern latitudes are Alfvénic, with small amplitudes (∼0.4nT), and are concentrated in wave packets similar to those observed in Kleindienst et al. (2009). The wave packets recur periodically at the northern magnetic oscillation period. We use a magnetospheric box model to provide an interpretation of the wave periods. Our model results suggest that the observed magnetic fluctuations are second harmonic Alfvén waves standing between the northern and southern ionospheres in Saturn's outer magnetosphere.
A possible precursor of the South China Sea summer monsoon onset: Effect of the South Asian High
Authors: Liu Boqi , Zhu Congwen
Published: October 2016

In climatology, the South China Sea (SCS) summer monsoon (SCSSM) generally onsets in Pentad 28 (16–20 May). The eastward extension of the South Asian High into the SCS in Pentad 27 is a possible precursor to the SCSSM onset. In the upper troposphere, the South Asian High (SAH) warms the air by inducing the positive potential vorticity advection, which strengthens precipitation over the southern SCS. When local convection becomes strong enough to decrease the vertical temperature gradient in Pentads 28–29, the upper level warming center overlies the subcloud warm region over the SCS to satisfy the requirement of the angular momentum conservation. A cross‐equatorial flow then forms, together with strong vertical easterly wind shear and deep monsoon convection over the SCS, marking the full establishment of the SCSSM. The abrupt change in the SAH in May could therefore be an early indicator of the onset of the SCSSM.
Alfvén wings in the lunar wake: The role of pressure gradients
Authors: Zhang H. , Khurana K. K. , Kivelson M. G. , Fatemi S. , Holmström M. , Angelopoulos V. , Jia Y. D. , Wan W. X. , Liu L. B. , Chen Y. D. , Le H. J. , Shi Q. Q. , Liu W. L.
Published: October 2016

Strongly conducting or magnetized obstacles in a flowing plasma generate structures called Alfvén wings, which mediate momentum transfer between the obstacle and the plasma. Nonconducting obstacles such as airless planetary bodies can generate such structures, which, however, have so far been seen only in sub‐Alfvénic regime. A novel statistical analysis of simultaneous measurements made by two ARTEMIS satellites, one in the solar wind upstream of the Moon and one in the downstream wake, and comparison of the data with results of a three‐dimensional hybrid model of the interaction reveal that the perturbed plasma downstream of the Moon generates Alfvén wings in super‐Alfvénic solar wind. In the wake region, magnetic field lines bulge toward the Moon and the plasma flows are significantly perturbed. We use the simulation to show that some of the observed bends of the field result from field‐aligned currents. The perturbations in the wake thus arise from a combination of compressional and Alfvénic perturbations. Because of the super‐Alfvénic background flow of the solar wind, the two Alfvén wings fold back to form a small intersection angle. The currents that form the Alfvén wing in the wake are driven by both plasma flow deceleration and a gradient of plasma pressure, positive down the wake from the region just downstream of the Moon. Such Alfvén wing structures, caused by pressure gradients in the wake and the resulting plasma slowdown, should exist downstream of any nonconducting body in a super‐Alfvénic plasma flow.
Prediction and predictability of land and atmosphere initialized CCSM4 climate forecasts over North America
Authors: Infanti Johnna M. , Kirtman Ben P.
Published: October 2016

Subseasonal‐to‐seasonal prediction is influenced by slowly varying surface fields such as sea surface temperature (SST) and soil moisture. Fully coupled hindcasts were recently completed in the Community Climate System Model version 4.0 (CCSM4) as part of the North American Multi‐Model Ensemble project. Using similar land and atmosphere initialization strategies, but with prescribed climatological SSTs, we attempt to determine the isolated impact of combined observed atmosphere and land initialization and of observed atmosphere initialization on monthly precipitation and 2 m temperature prediction‐estimated skill (i.e., skill assessed without SST variability) and predictability on monthly time scales. CCSM4 has been cited as having low land‐atmosphere coupling, and while combined land and atmosphere initialization significantly increases the estimated skill of precipitation and temperature in the first month after initialization (lead 0), land initialization influence is weak, consistent with low land‐atmosphere coupling in CCSM4. In contrast, atmosphere initialization is a stronger contributor to prediction skill and predictability. We find stronger influence of land and atmosphere initialization on precipitation in CCSM4 versus results from CCSM3. Predictability results show that there is potential skill to be gained for both precipitation and temperature should model errors, atmosphere or land initial state errors, and/or land‐atmosphere coupling improve.
Impacts of surface heterogeneity on dry planetary boundary layers in an urban‐rural setting
Authors: Zhu Xiaoliang , Ni Guangheng , Cong Zhentao , Sun Ting , Li Dan
Published: October 2016

Understanding the impacts of land use and land‐cover change such as urbanization is essential in many disciplines. This study investigates the impacts of urban‐rural contrasts in terms of momentum roughness length (z0) and aerodynamic surface temperature (TSK) on dry planetary boundary layers (PBLs) using large‐eddy simulations (LES) with the Weather Research and Forecasting (WRF) model. In addition, the impacts of small‐scale heterogeneities within urban areas are also examined. The original WRF‐LES is modified in order to use prescribed TSK as surface boundary conditions. Numerical simulations are then conducted to examine turbulence characteristics and mesoscale circulations resulting from large‐scale urban‐rural contrasts as well as small‐scale heterogeneities in urban areas. The results indicate that (1) the urban‐rural contrasts in z0 and TSK have significant but different impacts on surface heat fluxes, mesoscale circulations, and the wind and potential temperature profiles. Compared to the case where the whole domain is homogeneous, increases in z0 and/or TSK in urban areas in the center of domain induce stronger sensible heat fluxes, stronger urban circulations, and weaker inversions at the top of the PBL. (2) When the patch size that characterizes the urban heterogeneity scale is comparable to the size of the whole urban area, the simulated results are strongly dependent on both the heterogeneity scale and the specified surface temperature values. As the patch size decreases, the simulated results become more similar to those over a homogeneous urban surface.
Oceanic single‐layer warm clouds missed by the Cloud Profiling Radar as inferred from MODIS and CALIOP measurements
Authors: Liu Dongyang , Liu Qi , Qi Lin , Fu Yunfei
Published: October 2016

Attributed to its unique advantage of cloud vertical resolving, Cloud Profiling Radar (CPR) measurements have been used as the primary component in synthetic cloud data for relevant studies. However, due to surface clutter and sensitivity limitation, considerable warm clouds over global oceans are missed by CPR, which causes severe sampling biases and problematic statistics of cloud properties. By using independent cloud mask data jointly from Moderate Resolution Imaging Spectroradiometer and Cloud‐Aerosol Lidar with Orthogonal Polarization measurements, this study gives an evaluation on these issues and focuses on single‐layer clouds. By excluding effects from CPR's spatial resolution, the CPR detection failures are found to be frequent over global oceans, with an overall miss rate at ~0.39. For each cloud type, altocumulus, stratus, stratocumulus, and cumulus, its miss rate decreases monotonically with height, and it is only at 2.5–3.0 km altitude that the miss rate is negligible for the ensemble of oceanic single‐layer warm clouds. The miss rates are different among cloud types, which are attributed to their distinct microphysical properties. Clouds with droplet effective radius below 12 µm or cloud optical depth below 4 are very likely to be missed by CPR, resulting the globally averaged overestimation of 10–24% and 24–36%, respectively. The miss rate has a strong negative correlation with cloud water path (CWP) and decreases below 0.1 only for CWP exceeding 200 g m−2. The resulting overestimation on globally averaged CWP is 36.6 g m−2 (44.3%). Throughout the globe, the biases are mostly positive and have notable regional variations. Especially in the typical oceans that have abundant warm clouds, the CWP is overestimated by 20%–80%.
Bile acids and their oxo derivatives: Potential inhibitors of carbonic anhydrase I and II, androgen receptor antagonists and CYP3A4 substrates
Authors: Trifunović Jovana , Borčić Vladan , Mikov Momir
Published: October 2016

Some biological properties of bile acids and their oxo derivatives have not been sufficiently investigated, although the interest in bile acids as signaling molecules is rising. The aim of this work was to evaluate physico‐chemical parametar b (slope) that represents the lipophilicity of the examined molecules and to investigate interactions of bile acids with carbonic anhydrase I, II, androgen receptor and CYP450s. Thirteen candidates were investigated using normal‐phase thin‐layer chromatography in two solvent systems. Retention parameters were used in further quantitative structure–activity relationship analysis and docking studies to predict interactions and binding affinities of examined molecules with enzymes and receptors. Prediction of activity on androgen receptor showed that compounds 3α‐hydroxy‐12‐oxo‐5β‐cholanoic and 3α‐hydroxy‐7‐oxo‐5β‐cholanoic acid have stronger antiandrogen activity than natural bile acids. The inhibitory potential for carbonic anhydrase I and II was tested and it was concluded that molecules 3α‐hydroxy‐12‐oxo‐5β‐cholanoic, 3α‐hydroxy‐7‐oxo‐5β‐cholanoic, 3,7,12‐trioxo‐5β‐cholanoic acid and hyodeoxycholic acid show the best results. Substrate behavior for CYP3A4 was confirmed for all investigated compounds. Oxo derivatives of bile acids show stronger interactions with enzymes and receptors as classical bile acids and lower membranolytic activity compared with them. These significant observations could be valuable in consideration of oxo derivatives as building blocks in medicinal chemistry.
The role of microRNAs in islet β‐cell development
Authors: Kaviani Maryam , Azarpira Negar , Karimi Mohammad Hossein , Al‐Abdullah Ismail
Published: October 2016

Cell‐based therapies suggest novel treatments to overcome the complication of the current therapeutic approaches in diabetes mellitus type 1. Replacement of the destroyed pancreatic islet β‐cells by appropriate alternative cells needs an efficient approach to differentiate the cells into viable and functional insulin producing cells. Small non‐coding RNA molecules, microRNAs (miRNA), have critical roles in post‐transcriptional regulation of gene expression. Therefore, they can direct the cells toward β‐cell like cells and control islet β‐cell development. Previous reports showed the manipulation of the miRNA expression on islet β‐cell differentiation and regeneration. Likewise, the regulation of epithelial to mesenchymal transi­tion by the miR‐30 family and the miR‐200 family may be a useful approach to conduct islet β‐cell development. Investigation of stem cells differentiation showed that the dynamic expression patterns of miR‐375 and miR‐7 are similar to developing human fetal pancreas while dynamic expression of miR‐146a and miR‐34a occurred during the differentiation. Moreover, miR‐342 and its both targets, FOXA2 and MAFB, are found in β‐cell differentiation and maturation. Because miRNAs can target specific transcription factors during islet β‐cell development and differentiation, they could be offerred as alternative regenerative treatment for diabetes mellitus. Considering that the application of these non‐coding RNAs remains limited in the literature, in this review article, we present an overview of the roles of miRNAs in the islet β‐cell development, focusing on the application of different miRNAs in the experimental protocols.
Alkannin inhibits CCL3 and CCL5 production in human periodontal ligament cells
Authors: Hosokawa Yoshitaka , Hosokawa Ikuko , Shindo Satoru , Ohta Yoshihiro , Ozaki Kazumi , Matsuo Takashi
Published: October 2016

Alkannin, which is found in Alkanna tinctoria, a member of the borage family, is used as a food coloring. Alkannin has recently been reported to have certain biological functions, such as anti‐microbial and anti‐oxidant effects. It is known that CC chemokine receptor (CCR) 5‐positive leukocytes contribute to alveolar bone resorption in periodontal lesions. The aim of this study was to examine whether alkannin inhibits the production of CC chemokine ligand (CCL) 3 and CCL5, which are CCR5 ligands, in human periodontal ligament cells (HPDLC). Interleukin (IL)‐1β induced CCL3 and CCL5 production in HPDLC. Alkannin inhibited IL‐1β‐mediated CCL3 and CCL5 production in HPDLC in a dose‐dependent manner. Moreover, we revealed that alkannin suppressed inhibitor of kappa B‐α degradation in IL‐1β‐stimulated HPDLC. In addition, a nuclear factor (NF)‐κB inhibitor significantly inhibited CCL3 and CCL5 production in IL‐1β‐stimulated HPDLC. These results demonstrate that alkannin inhibits CCR5 ligand production in IL‐1β‐stimulated HPDLC by attenuating the NF‐κB signaling pathway.
Generation of improved human cerebral organoids from single copy DYRK1A knockout induced pluripotent stem cells in trisomy 21: hypothetical solutions for neurodevelopmental models and therapeutic alternatives in down syndrome
Authors: Çağlayan E. Sacide
Published: October 2016

Dual‐specificity thyrosine phosphorylation‐regulated kinase 1A (DYRK1A) is a strong therapeutic target to ameliorate cognitive functions of Down Syndrome (DS). Genetic normalization of Dyrk1a is sufficient to normalize early cortical developmental phenotypes in DS mouse models. Gyrencephalic human neocortical development is more complex than that in lissencephalic mice; hence, cerebral organoids (COs) can be used to model early neurodevelopmental defects of DS. Single copy DYRK1A knockout COs (scDYRK1AKO‐COs) can be generated from manipulated DS derived (DS‐) induced pluripotent stem cells (iPSCs) and genetic normalization of DYRK1A is expected to result in corrected neurodevelopmental phenotypes that can be reminiscent of normal COs. DYRK1A knock‐in (DYRK1AKI) COs can be derived after genetic manipulations of normal iPSCs and would be valuable to evaluate impaired neocortical development as can be seen in DS‐COs. DYRK1A mutations cause severe human primary microcephaly; hence, dose optimization studies of DYRK1A inhibitors will be critical for prenatal therapeutic applications in DS. Several doses of DYRK1A inhibitors can be tested in the neurodevelopment process of DS‐COs and DS‐scDYRK1AKO‐COs would be used as optimum models for evaluating phenotypic ameliorations. Overdose drug exposure in DS‐COs can be explained by similar defects present in DS‐baDYRK1AKO‐COs and DYRK1AKO‐COs. There are several limitations in the current CO technology, which can be reduced by the generation of vascularized brain‐like organoids giving opportunities to mimic late‐stage corticogenesis and complete hippocampal development. In the future, improved DS‐DYRK1AKO‐COs can be efficient in studies that aim to generate efficiently transplantable and implantable neurons for tissue regeneration alternatives in DS individuals.
Coupling Synergetic Effect between Ruthenium and Ruthenium Oxide with Size Effect of Ruthenium Particles on Ketone Catalytic Hydrogenation
Authors: Yang Zhao , Li Dan , Zhang Lei , Zheng Jinbao , Zhang Nuowei , Chen Bing H.
Published: October 2016

Carbon black‐supported ruthenium catalysts (Ru/C) with different Ru particle sizes and varying fractions of surficial RuO2 are prepared and studied for acetone hydrogenation. The size of Ru particles and the surficial RuO2 species on the Ru particles are found to affect the acetone conversion. Ru particles with larger size provide a higher catalytic activity suggesting an important role of particle size. Moreover, for Ru particles with larger sizes, the conversion decreases along with the increase of surficial RuO2 species fraction; however, an opposite trend is observed for cases with smaller Ru particles. Such distinguished catalytic acetone hydrogenation conversions for Ru/C with different particle sizes and varying surface RuO2 content suggest a size‐dependent synergetic effect, which, so far as we are concerned, is a new synergetic behavior between Ru and RuO2 in hydrogenation catalysis that has never been reported before. CO chemisorption, XRD, temperature‐programmed reduction, X‐ray photoelectron spectroscopy, and high‐resolution TEM are used to characterize the Ru particle sizes and the surficial RuO2 species.
Mesitylene‐Cored Glucoside Amphiphiles (MGAs) for Membrane Protein Studies: Importance of Alkyl Chain Density in Detergent Efficacy
Authors: Cho Kyung Ho , Ribeiro Orquidea , Du Yang , Tikhonova Elena , Mortensen Jonas S. , Markham Kelsey , Hariharan Parameswaran , Loland Claus J. , Guan Lan , Kobilka Brian K. , Byrne Bernadette , Chae Pil Seok
Published: October 2016

Detergents serve as useful tools for membrane protein structural and functional studies. Their amphipathic nature allows detergents to associate with the hydrophobic regions of membrane proteins whilst maintaining the proteins in aqueous solution. However, widely used conventional detergents are limited in their ability to maintain the structural integrity of membrane proteins and thus there are major efforts underway to develop novel agents with improved properties. We prepared mesitylene‐cored glucoside amphiphiles (MGAs) with three alkyl chains and compared these agents with previously developed xylene‐linked maltoside agents (XMAs) with two alkyl chains and a conventional detergent (DDM). When these agents were evaluated for four membrane proteins including a G protein‐coupled receptor (GPCR), some agents such as MGA‐C13 and MGA‐C14 resulted in markedly enhanced stability of membrane proteins compared to both DDM and the XMAs. This favourable behaviour is due likely to the increased hydrophobic density provided by the extra alkyl chain. Thus, this study not only describes new glucoside agents with potential for membrane protein research, but also introduces a new detergent design principle for future development.
Enhancing network I/o performance for a virtualized Hadoop cluster
Authors: Jeong Jinkyu , Choi Dong Hoon , Jo Heeseung
Published: October 2016

A MapReduce programming model is proposed to process big data using Hadoop, one of the major cloud computing frameworks. With the increasing adoption of cloud computing, running a Hadoop framework on a virtualized cluster is a compelling approach to reducing costs and increasing efficiency. In this paper, we measure the performance of a virtualized network and analyze the impact of network performance on Hadoop workloads running on a virtualized cluster. Then, we propose a virtualized network I/O architecture as a novel optimization for a virtualized Hadoop cluster for a public/private cloud provider. The proposed network architecture combines traditional network configurations and achieves better performance for Hadoop workloads. We also show a better way to utilize the rack awareness feature of the Hadoop framework in the proposed computing environment. The evaluation demonstrates that the proposed network architecture and mechanisms improve performance by up to 4.1 times compared with a bridge network architecture. This novel architecture can even virtually match the performance of the expensive, hardware‐based single root I/O virtualization network architecture.
PAWN: a payload‐based mutual authentication scheme for wireless sensor networks
Authors: Jan Mian , Nanda Priyadarsi , Usman Muhammad , He Xiangjian
Published: October 2016

Wireless sensor networks (WSNs) consist of resource‐starving miniature sensor nodes deployed in a remote and hostile environment. These networks operate on small batteries for days, months, and even years depending on the requirements of monitored applications. The battery‐powered operation and inaccessible human terrains make it practically infeasible to recharge the nodes unless some energy‐scavenging techniques are used. These networks experience threats at various layers and, as such, are vulnerable to a wide range of attacks. The resource‐constrained nature of sensor nodes, inaccessible human terrains, and error‐prone communication links make it obligatory to design lightweight but robust and secured schemes for these networks. In view of these limitations, we aim to design an extremely lightweight payload‐based mutual authentication scheme for a cluster‐based hierarchical WSN. The proposed scheme, also known as payload‐based mutual authentication for WSNs, operates in 2 steps. First, an optimal percentage of cluster heads is elected, authenticated, and allowed to communicate with neighboring nodes. Second, each cluster head, in a role of server, authenticates the nearby nodes for cluster formation. We validate our proposed scheme using various simulation metrics that outperform the existing schemes.
Astroturfing detection in social media: a binary n‐gram–based approach
Authors: Peng Jian , Detchon Sam , Choo Kim‐Kwang Raymond , Ashman Helen
Published: October 2016

Astroturfing is appearing in numerous contexts in social media, with individuals posting product reviews or political commentary under a number of different names, and is of concern because of the intended deception. An astroturfer works with the aim of making it seem that a large number of people hold the same opinion, promoting a consensus based on the astroturfer's intentions. It is generally done for commercial or political advantage, often by paid writers or ideologically motivated writers. This paper brings the notion of authorship attribution to bear on the astroturfing problem, collecting quantities of data from public social media sites and analyzing the putative individual authors to see if they appear to be the same person. The analysis comprises a binary n‐gram method, which was previously shown to be effective at accurately identifying authors on a training set from the same authors, while this paper shows how authors on different social media turn out to be the same author. The method has identified numerous instances where multiple accounts are apparently being operated by a single individual.
Enhanced similarity measure for personalized cloud services recommendation
Authors: Afify Y.M. , Moawad I.F. , Badr N.L. , Tolba M.F.
Published: October 2016

Cloud users are overwhelmed with great numbers of cloud services. Service recommender systems evaluate the services that provide same functionalities according to the user requirements. A key enabler to accurate recommendation in recommender systems is the appropriate determination of similar users. This paper contributes to the personalized cloud services recommendation area. In specific, we introduce a user‐based similarity measure that integrates relevant similarity aspects: user demographic information, service ratings, and user interest. The proposed similarity measure is used in a hybrid collaborative filtering (CF) approach that leverages the advantages of both model‐ and memory‐based approaches to improve the recommendation process. Experimental evaluation on real‐world services data set shows that the proposed approach outperforms other CF approaches in respect of the prediction accuracy and recommendation time while maintaining better or same coverage.
Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia
Authors: Wadley Jessica J. , Fordham Damien A. , Thomson Vicki A. , Ritchie Euan G. , Austin Jeremy J.
Published: October 2016

The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species’ range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re‐examine these results to (1) determine phylogeographic patterns across the range of M. antilopinus and (2) infer the biogeographic barriers associated with these patterns. The tropical savannahs of northern Australia: from the Cape York Peninsula in the east, to the Kimberley in the west. We examined phylogeographic patterns in M. antilopinus using a larger number of samples and three mtDNA genes: NADH dehydrogenase subunit 2, cytochrome b, and the control region. Two datasets were generated and analyzed: (1) a subset of samples with all three mtDNA regions concatenated together and (2) all samples for just control region sequences that included samples from the previous study. Analysis included generating phylogenetic trees based on Bayesian analysis and intraspecific median‐joining networks. The contemporary spatial structure of M. antilopinus mtDNA lineages revealed five shallow clades and a sixth, divergent lineage. The genetic differences that we found between Queensland and Northern Territory M. antilopinus samples confirmed the split in the geographic distribution of the species. We also found weak genetic differentiation between Northern Territory samples and those from the Kimberley region of Western Australia, possibly due to the Kimberley Plateau–Arnhem Land barrier. Within the Northern Territory, two clades appear to be parapatric in the west, while another two clades are broadly sympatric across the Northern Territory. MtDNA diversity of M. antilopinus revealed an unexpectedly complex evolutionary history involving multiple sympatric and parapatric mtDNA clades across northern Australia. These phylogeographic patterns highlight the importance of investigating genetic variation across distributions of species and integrating this information into biodiversity conservation.
Temperature effects on mass‐scaling exponents in colonial animals: a manipulative test
Authors: Barneche Diego R. , White Craig R. , Marshall Dustin J.
Published: October 2016

Body size and temperature are fundamental drivers of ecological processes because they determine metabolic rates at the individual level. Whether these drivers act independently on individual‐level metabolic rates remains uncertain. Most studies of intraspecific scaling of unitary organisms must rely on preexisting differences in size to examine its relationship with metabolic rate, thereby potentially confounding size‐correlated traits (e.g., age, nutrition) with size, which can affect metabolic rate. Here, we use a size manipulation approach to test whether metabolic mass scaling and temperature dependence interact in four species (two phyla) of colonial marine invertebrates. Size manipulation in colonial organisms allows tests of how ecological processes (e.g., predation) affect individual physiology and consequently population‐ and community‐level energy flux. Body mass and temperature interacted in two species, with one species exhibiting decreased and the other increased mass‐scaling exponents with increasing temperature. The allometric scaling of metabolic rate that we observe in three species contrasts with the isometric scaling of ingestion rates observed in some colonial marine invertebrates. Thus, we suggest that the often observed competitive superiority of colonial over unitary organisms may arise because the difference between energy intake and expenditure increases more strongly with size in colonial organisms.
Pump‐Pump‐Probe Spectroscopy of a Molecular Triad Monitoring Detrimental Processes for Photoinduced Charge Accumulation
Authors: Kuss‐Petermann Martin , Wenger Oliver S.
Published: October 2016

Controlling light‐induced accumulation of electrons or holes is desirable in view of multi‐electron redox chemistry, for example for the formation of solar fuels or for photoredox catalysis in general. Excitation with multiple photons is usually required for electron or hole accumulation, and consequently pump‐pump‐probe spectroscopy becomes a valuable spectroscopic tool. In this work, we excited a triarylamine‐Ru(bpy)32+‐anthraquinone triad (bpy = 2,2′‐bipyridine) with two temporally delayed laser pulses of different color and monitored the resulting photoproducts. Absorption of the first photon by the Ru(bpy)32+ photosensitizer generated a triarylamine radical cation and an anthraquinone radical anion by intramolecular electron transfer. Subsequent selective excitation of either one of these two radical ion species then induced rapid reverse electron transfer to yield the triad in its initial (ground) state. This shows in direct manner that after absorption of a first photon and formation of the primary photoproducts, the absorption of a second photon can lead to unproductive electron transfer events that counteract further charge accumulation. In principle, this problem is avoidable by careful excitation wavelength selection in combination with good molecular design.
Geolithological and anthropogenic controls on the hydrochemistry of the Volturno river (Southern Italy)
Authors: Cuoco Emilio , Colombani Nicolò , Darrah Thomas H. , Mastrocicco Micòl , Tedesco Dario
Published: October 2016

The present work aims to study the main chemical and physical water parameters in the upper and middle Volturno river catchment (southern Italy), between the Capo Volturno springs and the confluence with the Calore river. This study makes use of morphology, geolithology, tectonic, land use, and physico‐chemical (pH, electrical conductivity, redox potential, temperature, major ions, and 222Rn) data for the identification of the main sources of surface and groundwaters in the Volturno catchment and of their evolution and mixing both in base flow and peak flow conditions. The study was also performed to assess whether the alteration due to potential anthropogenic contamination may hamper the identification of natural “primitive” sources of surface waters, especially in the populated and farmed plains far from the river headwaters. Our data suggest that water chemistry of this stretch of the Volturno river is dominated mainly by lithology and, only marginally, by the intense exogenous activities and that this trend is appreciable in both base flow and peak flow conditions. The proposed simple geochemical approach based on easy‐to‐sample matrices and on cost‐effective standard methods is a valuable tool to address catchment functionality especially in upland areas, where complex geologic and structural settings, heterogeneous groundwater flow, and logistical issues are the rule rather than the exception. Because the upper and middle Volturno catchment is comparable with numerous valleys of the Mediterranean area, this study could be a reference for analogous applications.
Hydraulic modeling of flood pulses in the Middle Bussento Karst System (MBSKS), UNESCO Cilento Global Geopark, southern Italy
Authors: Bovolin Vittorio , Cuomo Albina , Guida Domenico
Published: October 2016

Karst systems provide water for domestic and industrial uses and for generating hydropower, but they can also create fluvial hazards, such as upstream back‐flooding and downstream karst flash‐flood events. However, these hazards are difficult to foresee due to the complex recharge‐discharge processes as well as the lack of information on the inside of the system, which has often not been completely surveyed by speleologists or explored by boreholes. To overcome these difficulties, hydro‐chemical data from the monitoring system in the Middle Bussento Karst System (MBSKS), one of the first Experimental Karst Systems in southern Italy, were recorded and previously discussed. Based on shared background in flood karst hydraulic modeling, this paper describes the conceptual premises and rationale of a general‐purpose hydraulic model that is suitable both for the MBSKS and for other Mediterranean, multi‐recharge, mature, conduit‐dominated karst systems. To test the reliability of the model, simulations of time–space behavior and response are performed using natural and artificial flood pulses “as tracers”, considering a “pulse” as a significant variation in water quantity and/or quality. The results of the model explain the interactions between allogenic, autogenic, and anthropogenic recharges from differentiated sources and phreatic conduit systems. These results also clarify the overall response of karst springs at typical time scales of flood pulses.

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An improved method for calculating toxicity-based pollutant loads: Part 1. Method development
Authors: Smith Rachael A , Warne Michael St J , Mengersen Kerrie , Turner Ryan DR
Published: October 2016

Pollutant loads are a means for assessing regulatory compliance and setting targets to reduce pollution entering receiving waterbodies. However, a pollutant load is often comprised of multiple chemicals, which may exert joint toxicity on biota. When the ultimate goal for assessing pollutant loads is to protect ecosystems from adverse effects of toxicants, then the total pollutant load needs to be calculated based on the principles of mixture toxicology. In this article, an improved method is proposed to convert a pollutant load to a toxicity-based load (toxic load) using a modified toxic equivalency factor (TEF) derivation method. The method uses the relative potencies (RePs) of multiple species to represent the response of the ecological community. The TEF is calculated from a percentile of a cumulative distribution function (CDF) fitted to the RePs. The improvements permit the determination of which percentile of the CDF generates the most environmentally relevant and robust toxic loads. That is, environmental relevance ensures that a reduction in the toxic load is likely to result in a corresponding improvement in ecosystem health and robustness ensures that the calculation of the toxic loads is not biased by the reference chemical used. The improved methodology will therefore ensure that correct management decisions will be made and ultimately, a reduction in the toxic load will lead to a commensurate improvement in water quality. Integr Environ Assess Manag 2017;13:746–753. © 2016 SETAC

Key Points

We present an improved method for converting pollutant loads of chemical mixtures to a total pollutant load based on the toxicities of the constituents (i.e., the “toxic load”), aiding water quality managers to assess and regulate the whole pollutant load rather than each chemical load separately. The method is a modified toxic equivalency factor (TEF) approach that uses the relative potencies of multiple species to calculate a TEF to weight each pollutant load based on its relative toxicity to a reference chemical. The modified TEF approach presents 2 novel tests, for environmental relevance and robustness, to determine which percentile of the cumulative distribution of relative potencies should be used to calculate the TEF to generate the most environmentally relevant and robust toxic loads. Calculating toxic loads makes ecotoxicological sense when dealing with mixtures of toxicants and will inform water quality managers on which chemicals and regions they should focus their actions, leading to better allocation of resources.
Characterization of Burkholderia sp. XTB‐5 for Phenol Degradation and Plant Growth Promotion and Its Application in Bioremediation of Contaminated Soil
Authors: Chen Jun , Li Songshuo , Xu Bin , Su Cuizhu , Jiang Qiuyue , Zhou Chenhao , Jin Qing , Zhao Yu , Xiao Ming
Published: October 2016

A key issue when researching land degradation is the pollution of soils. For bioremediation of contaminated soil, Burkholderia sp. XTB‐5 cells were obtained from soil and grown on mineral salt medium with initial phenol concentrations of 650 mg L−1 and 850 mg L−1, which were found to degrade more than 98% of phenol content in less than 4 days. About 90% of phenol content (with initial concentration of 250 mg kg−1 soil) was removed from soil inoculated with XTB‐5 cells in 6 days. More than 90% of phenol content was removed within 20 days after co‐introduction of XTB‐5 cells and plants to sterilized soil in a greenhouse or to natural soil in field trials. But under the same conditions, individual introduction of plants to sterilized soil in the greenhouse reduced phenol content by about 50% and introduction to natural soil in field trials reduced phenol content by about 38%, suggesting that phytoremediation of phenol is often inefficient and microorganisms can efficiently degrade this pollutant. In addition, strain XTB‐5 was found to solubilize phosphate and produce 1‐Aminocyclopropane‐1‐Carboxylate (ACC) deaminase and siderophore. Strain XTB‐5 promoted plant growth in both phenol‐absent and phenol‐spiked soil under greenhouse and field conditions. Considering that ACC deaminase is beneficial to plant growth under adverse environmental conditions, plant growth promotion by XTB‐5 in phenol‐contaminated soil is not only due to XTB‐5 cell‐degradation of phenol and reduced phytotoxicity but also to production of ACC deaminase. Hence, Burkholderia sp. XTB‐5 presents an attractive microorganism for phytoremediation of contaminated soil and agronomic application. Copyright © 2016 John Wiley & Sons, Ltd.