bluuebunny/crossref_metadata_2025 huggingface dataset:
Vesiculation and Quenching During Surtseyan Eruptions at Hunga Tonga‐Hunga Ha'apai Volcano, Tonga
Authors: Colombier M. , Scheu B. , Wadsworth F. B. , Cronin S. , Vasseur J. , Dobson K. J. , Hess K.‐U. , Tost M. , Yilmaz T. I. , Cimarelli C. , Brenna M. , Ruthensteiner B. , Dingwell D. B.
Published: May 2018

Surtseyan eruptions are shallow to emergent subaqueous explosive eruptions that owe much of their characteristic behavior to the interaction of magma with water. The difference in thermal properties between water and air affects the cooling and postfragmentation vesiculation processes in magma erupted into the water column. Here we study the vesiculation and cooling processes during the 2009 and 2014–2015 Surtseyan eruptions of Hunga Tonga‐Hunga Ha'apai volcano by combining 2‐D and 3‐D vesicle‐scale analyses of lapilli and bombs and numerical thermal modeling. Most of the lapilli and bombs show gradual textural variations from rim to core. The vesicle connectivity in the lapilli and bombs increases with vesicularity from fully isolated to completely connected and also increases from rim to core in transitional clasts. We interpret the gradual textural variations and the connectivity‐vesicularity relationships as the result of postfragmentation bubble growth and coalescence interrupted at different stages by quenching in water. The measured vesicle size distributions are bimodal with a population of small and large vesicles. We interpret this bimodality as the result of two nucleation events, one prefragmentation with the nucleation and growth of large bubbles and one postfragmentation with nucleation of small vesicles. We link the thermal model with the textural variations in the clasts—showing a dependence on particle size, Leidenfrost effect, and initial melt temperature. In particular, the cooling profiles in the bombs are consistent with the gradual textural variations from rim to core in the clasts, likely caused by variations in time available for vesiculation before quenching.
Multicentury Instability of the Atlantic Meridional Circulation in Rapid Warming Simulations With GISS ModelE2
Authors: Rind David , Schmidt Gavin A. , Jonas Jeff , Miller Ron , Nazarenko Larissa , Kelley Max , Romanski Joy
Published: May 2018

In multimillennial global warming simulations with the GISS‐E2‐R climate model, we observe multicentennial shutdowns with restoration and fast overshooting in North Atlantic Deep Water production despite the absence of exogenous freshwater input. AMOC (Atlantic Meridional Overturning Circulation) cessation is associated with a sea surface salinity reduction, initiated by increases in precipitation over evaporation as the climate warms. These multicentury shutdowns are the direct result of cooling in the North Atlantic associated with an aerosol indirect effect on cloud cover. The local cooling reduces evaporation within the North Atlantic, while warming elsewhere provides moisture to maintain nearly unperturbed precipitation in this region. As global warming continues, warm temperature (low density) anomalies spread northward at depth in the North Atlantic eventually destabilizing the water column, even though precipitation input at the surface is initially unchanged. Internal ocean freshwater transports do not play an important role in initiating this behavior, as assumed by some standard metrics of AMOC stability. The importance of the aerosol indirect effect in these runs is due to its role in strengthening the sea surface temperature‐evaporation feedback; this suggests a renewed focus on surface flux observations to help assess overturning stability. The length of the AMOC reduction, and its rapid recovery, may be relevant to the onset and end of the Younger Dryas, which occurred within a warming climate during the last deglaciation.
Evaluation of Agricultural Land Cover Representations on Regional Climate Model Simulations in the Brazilian Cerrado
Authors: Spera Stephanie A. , Winter Jonathan M. , Chipman Jonathan W.
Published: May 2018

Examining interactions between large‐scale land cover and land use change and regional climate in areas undergoing dynamic land transformations, like the Brazilian Cerrado, is crucial for understanding tradeoffs between human needs and ecosystem services. Yet regional climate models often do not include accurate land cover data of these complex landscapes. We use National Center for Atmospheric Research's Weather Research and Forecasting (WRF) model coupled to the Noah‐Multiparameterization (Noah‐MP) land surface model to run 10‐year climate simulations across Brazil to assess (1) whether an accurate, regionally validated land cover data set with two, new agricultural land cover classifications improves model simulation results; (2) the ability of Noah‐MP's dynamic vegetation option to model vegetation growth; and (3) the sensitivity of the model output to scale. The results of the simulations with the updated land surface perform better over intensive agricultural areas for precipitation, evapotranspiration, and temperature, especially during the wet‐to‐dry season transition months. Evapotranspiration is overestimated during the start of the rainy season across all model simulations, which is likely due to the soil moisture model. We also find that using the Noah‐MP dynamic vegetation significantly degrades agricultural leaf area index phenology simulations in Brazilian agricultural regions. Lastly, improving the model's resolution did not improve model output when compared to observational data. Incorporating more accurate representations of the landscape into regional climate models is essential for quantifying potential changes in climatological seasonality in dynamic, human‐modified regions and making informed land use decisions.
The Influence of Real‐World Wind Turbine Deployments on Local to Mesoscale Climate
Authors: Pryor S. C. , Barthelmie R. J. , Shepherd T. J.
Published: May 2018

Paired simulations are conducted using the Weather Research and Forecasting model applied at convection permitting resolution in order to determine the impact of wind turbines (WTs) on the local to mesoscale climate. Using actual WT locations and a model of the effect of the WT rotor on the flow field, it is shown that while the presence of WT changes wind speeds (WSs) and near‐surface air temperature in 4‐km grid cells in which WTs are located, the impact at larger scales on near‐surface air temperature, specific humidity, the fluxes of latent and sensible heat, boundary layer heights, and precipitation is not significant in any season other than summer. During summer, the maximum pairwise difference in grid cell mean temperatures is 0.5 K and the maximum increase in near‐surface specific humidity is 0.4 g/kg. However, a spatial average of the mean seasonal perturbation of air temperature by WT gives a net impact of <0.1 K. Precipitation probability is also not significantly impacted in any season other than summer. In the summer the presence of WT is associated with a small decrease in precipitation probability and a decrease in season total precipitation of −2.6%. The finding of minor magnitude, but significant impacts, during summer should be used to contextualize results of substantial climate impacts from WT arrays deployed in the U.S. Central Plains based on short‐term simulations conducted for the summer season.
The Influence of Curvature on Convection in a Temperature‐Dependent Viscosity Fluid: Implications for the 2‐D and 3‐D Modeling of Moons
Authors: Guerrero J. M. , Lowman J. P. , Deschamps F. , Tackley P. J.
Published: May 2018

Convection in terrestrial bodies occurs within spherical shells described by the ratio, f, of their bounding radii. Previous studies that have modeled convection with a temperature‐dependent viscosity noted the strong effect of f on transition to the stagnant‐lid regime. Here we analyze stagnant‐lid convection in 2‐D and 3‐D systems with curvatures including relatively small‐core shells (f as small as 0.2) as well as in thin shell and plane‐layer cases. Several peculiarities of convection in a strongly temperature‐dependent viscosity fluid are identified for both high and low curvature systems. We demonstrate that effective Rayleigh numbers may differ by orders of magnitude in systems with different curvatures, when all other parameters are maintained at fixed values. Furthermore, as f is decreased, the nature of stagnant‐lid convection in small‐core bodies shows a divergence in the temperature and velocity fields found for 2‐D annulus and 3‐D spherical shell systems. In addition, substantial differences in the behavior of thin shell (f = 0.9) and plane‐layer (Cartesian geometry) models occur in both 2‐D and 3‐D, indicating that the latter (emulating a toroidal topology rather than spherical) may be inappropriate approximations for modeling variable viscosity convection in thin spherical shells. Our findings are especially relevant to understanding and accurately modeling the thermal structure that may exist in bodies characterized by thin shells (e.g., f = 0.9) or relatively small cores, such as shells comprising the Galilean satellites and other moons.
The Response of African Equatorial/Low‐Latitude Ionosphere to 2015 St. Patrick's Day Geomagnetic Storm
Authors: Amaechi P. O. , Oyeyemi E. O. , Akala A. O.
Published: May 2018

Total electron content (TEC) has been used to study the response of the African equatorial/low‐latitude ionosphere to the 17 March 2015 intense storm. Daily variations of symmetric H index, z component of interplanetary magnetic field, polar cap index, and H component of the Earth's magnetic field were analyzed along with TEC obtained from stations classified into western (11.53°E to 5.24°W) and eastern (25.00°E to 40.20°E) sectors. Storm time behavior of TEC was compared with the mean TEC of quiet days. TEC was enhanced over both sectors at the beginning of the storm while it reduced after the main phase as a result of prompt penetration of electric field and disturbance dynamo electric field (DDEF), respectively. The magnetic effect of the disturbed ionospheric electric current showed oscillations and minima in response to prompt penetration of electric field, which further enhanced the equatorial ionization anomaly. The effect of DDEF estimated from the ionospheric disturbance dynamo manifested in the form of decrease in the amplitude of the horizontal component of the Earth magnetic field (H) several hours after the beginning of the disturbance and during the recovery phase. Consequently, ionospheric irregularities were suppressed over all stations in both sectors on 17 and 18 March due to westward DDEF. On the 19 March, however, there was a difference in the pattern of irregularities over both sectors.
A Consistent Model of Ice Dissociation on Celestial Bodies
Authors: Cook Terri
Published: May 2018

A model based on decades of experimental results can now quantify the products of water ice dissociation caused by radiation and predict the products expelled into an icy body’s outer atmosphere.
Can the Updip Limit of Frictional Locking on Megathrusts Be Detected Geodetically? Quantifying the Effect of Stress Shadows on Near‐Trench Coupling
Authors: Almeida Rafael , Lindsey Eric O. , Bradley Kyle , Hubbard Judith , Mallick Rishav , Hill Emma M.
Published: May 2018

The updip limit of the seismogenic zone of megathrusts is poorly understood. The relative absence of observed microseismicity in such regions, together with laboratory studies of friction, suggests that the shallow fault is mostly velocity strengthening, and likely to creep. Inversions of geodetic data commonly show low to zero coupling at the trench, reinforcing this view. We show that the locked, downdip portion of the megathrust creates an updip stress shadow that prevents the shallow portion of the fault from creeping at a significant rate, regardless of its frictional behavior. Our models demonstrate that even if the shallowest 40% of the fault is frictionally unlocked, the expected creep at the fault tip is at most 30% of the plate rate, often within the uncertainties of surface geodetic measurements, and below current resolution of seafloor measurements. We conclude that many geodetic models significantly underestimate the degree of shallow coupling on megathrusts, and thus seismic and tsunami hazard.
Multiple convergent supergene evolution events in mating-type chromosomes
Authors: Branco Sara , Carpentier Fantin , Rodríguez de la Vega Ricardo C. , Badouin Hélène , Snirc Alodie , Le Prieur Stéphanie , Coelho Marco A. , de Vienne Damien M. , Hartmann Fanny E. , Begerow Dominik , Hood Michael E. , Giraud Tatiana
Published: May 2018

Convergent adaptation provides unique insights into the predictability of evolution and ultimately into processes of biological diversification. Supergenes (beneficial gene linkage) are striking examples of adaptation, but little is known about their prevalence or evolution. A recent study on anther-smut fungi documented supergene formation by rearrangements linking two key mating-type loci, controlling pre- and post-mating compatibility. Here further high-quality genome assemblies reveal four additional independent cases of chromosomal rearrangements leading to regions of suppressed recombination linking these mating-type loci in closely related species. Such convergent transitions in genomic architecture of mating-type determination indicate strong selection favoring linkage of mating-type loci into cosegregating supergenes. We find independent evolutionary strata (stepwise recombination suppression) in several species, with extensive rearrangements, gene losses, and transposable element accumulation. We thus show remarkable convergence in mating-type chromosome evolution, recurrent supergene formation, and repeated evolution of similar phenotypes through different genomic changes.
A workflow for the integrative transcriptomic description of molecular pathology and the suggestion of normalizing compounds, exemplified by Parkinson’s disease
Authors: Hamed Mohamed , Gladbach Yvonne , Möller Steffen , Fischer Sarah , Ernst Mathias , Struckmann Stephan , Storch Alexander , Fuellen Georg
Published: May 2018

The volume of molecular observations on human diseases in public databases is continuously increasing at accelerating rates. A bottleneck is their computational integration into a coherent description, from which researchers may derive new well-founded hypotheses. Also, the need to integrate data from different technologies (genetics, coding and regulatory RNA, proteomics) emerged in order to identify biomarkers for early diagnosis and prognosis of complex diseases and therefore facilitating the development of novel treatment approaches. We propose here a workflow for the integrative transcriptomic description of the molecular pathology in Parkinsons’s Disease (PD), including suggestions of compounds normalizing disease-induced transcriptional changes as a paradigmatic example. We integrated gene expression profiles, miRNA signatures, and publicly available regulatory databases to specify a partial model of the molecular pathophysiology of PD. Six genetic driver elements (2 genes and 4 miRNAs) and several functional network modules that are associated with PD were identified. Functional modules were assessed for their statistical significance, cellular functional homogeneity, literature evidence, and normalizing small molecules. In summary, our workflow for the joint regulatory analysis of coding and non-coding RNA, has the potential to yield clinically as well as biologically relevant information, as demonstrated here on PD data.
A direct tissue-grafting approach to increasing endogenous brown fat
Authors: Blumenfeld Nicole R. , Kang Hwan June , Fenzl Anna , Song Ziwei , Chung Janice J. , Singh Ranjodh , Johnson Roshawn , Karakecili Ayse , Feranil Jun B. , Rossen Ninna S. , Zhang Vivian , Jaggi Sahir , McCarty Bret , Bessler Steven , Schwartz Gary J. , Grant Robert , Korner Judith , Kiefer Florian W. , Gillette Brian M. , Sia Samuel K.
Published: May 2018

There is widespread evidence that increasing functional mass of brown adipose tissue (BAT) via browning of white adipose tissue (WAT) could potentially counter obesity and diabetes. However, most current approaches focus on administration of pharmacological compounds which expose patients to highly undesirable side effects. Here, we describe a simple and direct tissue-grafting approach to increase BAT mass through ex vivo browning of subcutaneous WAT, followed by re-implantation into the host; this cell-therapy approach could potentially act synergistically with existing pharmacological approaches. With this process, entitled “exBAT”, we identified conditions, in both mouse and human tissue, that convert whole fragments of WAT to BAT via a single step and without unwanted off-target pharmacological effects. We show that ex vivo, exBAT exhibited UCP1 immunostaining, lipid droplet formation, and mitochondrial metabolic activity consistent with native BAT. In mice, exBAT exhibited a highly durable phenotype for at least 8 weeks. Overall, these results enable a simple and scalable tissue-grafting strategy, rather than pharmacological approaches, for increasing endogenous BAT and studying its effect on host weight and metabolism.
Differential protein profiling as a potential multi-marker approach for obese patients with heart failure: A retrospective study
Authors: Timotin Andrei , Cinato Mathieu , Boal Frederic , Dejean Sebastien , Anesia Rodica , Arnaut Oleg , Lagente Christine , Roncalli Jerome , Desmoulin Franck , Tronchere Helene , Kunduzova Oksana
Published: May 2018

Identification of novel circulating biomarkers predicting death and major cardio-metabolic events in obese patients with heart failure (HF) remains a research priority. In this study, we compared multi-marker profile of non-obese (NOB) and obese (OB) HF patients in relation to mortality outcome. The new multiplex proximity extension assay technology was used to analyze the levels of 92 proteins in plasma samples from HF patients according to body mass index (BMI) categories. At 2-year follow-up, all-cause mortality rates were significantly greater in NOB patients (BMI < 30 kg/m2) compared to the OB patients (BMI > 30 kg/m2) with HF (odds ratio 26; 95% CI: 1.14–624, p < 0,04). Quantitative proteomic analysis revealed thirteen distinct proteins expression profiles of OB and NOB HF patients. Among these proteins, RAGE, CXCL6, CXCL1, CD40, NEMO, VEGF-A, KLK6, PECAM1, PAR1, MMP1, BNP and NTproBNP were down-regulated, whereas leptin was up-regulated in OB HF patients. In addition, an inverse correlation between plasma BNP levels and leptin in OB HF patients was observed (r = −0.58 p = 0.02). This study identifies specific plasma protein signature in OB and NOB patients with HF in relation to mortality outcome.
Statistical machine learning of sleep and physical activity phenotypes from sensor data in 96,220 UK Biobank participants
Authors: Willetts Matthew , Hollowell Sven , Aslett Louis , Holmes Chris , Doherty Aiden
Published: May 2018

Current public health guidelines on physical activity and sleep duration are limited by a reliance on subjective self-reported evidence. Using data from simple wrist-worn activity monitors, we developed a tailored machine learning model, using balanced random forests with Hidden Markov Models, to reliably detect a number of activity modes. We show that physical activity and sleep behaviours can be classified with 87% accuracy in 159,504 minutes of recorded free-living behaviours from 132 adults. These trained models can be used to infer fine resolution activity patterns at the population scale in 96,220 participants. For example, we find that men spend more time in both low- and high- intensity behaviours, while women spend more time in mixed behaviours. Walking time is highest in spring and sleep time lowest during the summer. This work opens the possibility of future public health guidelines informed by the health consequences associated with specific, objectively measured, physical activity and sleep behaviours.
Extremely Low Frequency Electromagnetic Fields impair the Cognitive and Motor Abilities of Honey Bees
Authors: Shepherd S. , Lima M. A. P. , Oliveira E. E. , Sharkh S. M. , Jackson C. W. , Newland P. L.
Published: May 2018

Extremely low frequency electromagnetic field (ELF EMF) pollution from overhead powerlines is known to cause biological effects across many phyla, but these effects are poorly understood. Honey bees are important pollinators across the globe and due to their foraging flights are exposed to relatively high levels of ELF EMF in proximity to powerlines. Here we ask how acute exposure to 50 Hz ELF EMFs at levels ranging from 20–100 µT, found at ground level below powerline conductors, to 1000–7000 µT, found within 1 m of the conductors, affects honey bee olfactory learning, flight, foraging activity and feeding. ELF EMF exposure was found to reduce learning, alter flight dynamics, reduce the success of foraging flights towards food sources, and feeding. The results suggest that 50 Hz ELF EMFs emitted from powerlines may represent a prominent environmental stressor for honey bees, with the potential to impact on their cognitive and motor abilities, which could in turn reduce their ability to pollinate crops.
Genome-wide association study identified new susceptible genetic variants in HLA class I region for hepatitis B virus-related hepatocellular carcinoma
Authors: Sawai Hiromi , Nishida Nao , Khor Seik-Soon , Honda Masao , Sugiyama Masaya , Baba Natsumi , Yamada Kayoko , Sawada Norie , Tsugane Shoichiro , Koike Kazuhiko , Kondo Yuji , Yatsuhashi Hiroshi , Nagaoka Shinya , Taketomi Akinobu , Fukai Moto , Kurosaki Masayuki , Izumi Namiki , Kang Jong-Hon , Murata Kazumoto , Hino Keisuke , Nishina Sohji , Matsumoto Akihiro , Tanaka Eiji , Sakamoto Naoya , Ogawa Koji , Yamamoto Kazuhide , Tamori Akihiro , Yokosuka Osamu , Kanda Tatsuo , Sakaida Isao , Itoh Yoshito , Eguchi Yuichiro , Oeda Satoshi , Mochida Satoshi , Yuen Man-Fung , Seto Wai-Kay , Poovorawan Yong , Posuwan Nawarat , Mizokami Masashi , Tokunaga Katsushi
Published: May 2018

We have performed a genome-wide association study (GWAS) including 473 Japanese HBV (hepatitis B virus)-positive HCC (hepatocellular carcinoma) patients and 516 HBV carriers including chronic hepatitis and asymptomatic carrier individuals to identify new host genetic factors associated with HBV-derived HCC in Japanese and other East Asian populations. We identified 65 SNPs with P values < 10−4 located within the HLA class I region and three SNPs were genotyped in three independent population-based replication sets. Meta-analysis confirmed the association of the three SNPs (rs2523961: OR = 1.73, P = 7.50 × 10−12; rs1110446: OR = 1.79, P = 1.66 × 10−13; and rs3094137: OR = 1.73, P = 7.09 × 10−9). We then performed two-field HLA genotype imputation for six HLA loci using genotyping data to investigate the association between HLA alleles and HCC. HLA allele association testing revealed that HLA-A
*
33:03 (OR = 1.97, P = 4.58 × 10−4) was significantly associated with disease progression to HCC. Conditioning analysis of each of the three SNPs on the HLA class I region abolished the association of HLA-A*33:03 with disease progression to HCC. However, conditioning the HLA allele could not eliminate the association of the three SNPs, suggesting that additional genetic factors may exist in the HLA class I region.
Allergy immunotherapy restores airway epithelial barrier dysfunction through suppressing IL-25 -induced endoplasmic reticulum stress in asthma
Authors: Yuan Xiefang , Wang Junyi , Li Yin , He Xiang , Niu Bin , Wu Dehong , lan Nan , Wang Xiaoyun , Zhang Yun , Dai Xi , Wang Xing , Liu Zhigang , Li Guoping
Published: May 2018

Constant exposure to allergen triggers destructive type 2 cell-mediated inflammation. The effect of allergen specific immunotherapy (SIT) in maintaining airway epithelial barrier function in asthma remains unknown. In the current study, we showed that SIT maintained airway epithelial homeostasis in mice exposed to dermatophagoides farinae (Der f), which induced increased expression of IL-25, endoplasmic reticulum (ER) stress and airway epithelial apoptosis. Meanwhile, SIT treatment ameliorated airway inflammatory infiltration and hyper-responsiveness in allergic mice. SIT treatment restored the airway epithelial integrity, attenuated Der f -induced airway epithelial ER stress and epithelial apoptosis. We also found that 4-PBA, an inhibitor of ER stress, suppressed airway epithelial ER stress and apoptosis in vitro. The pathological changes were partially induced by IL-25-induced ER stress, epithelial tight junction damage, and cell apoptosis in airways following allergen exposure. Furthermore, IL-25 induced ER stress in airway epithelial cells in vitro. The IL-25-induced airway epithelial apoptosis dependent on PERK activity was inhibited by 4-PBA. Taken together, we demonstrate that SIT is effective in allergic asthma and dependent on its depressive effect on the expression of IL-25, epithelial integrity damage, and epithelial ER stress.
Commercially Available Natural Benzyl Esters and Their Synthetic Analogs Exhibit Different Toxicities against Insect Pests
Authors: Feng Yan , Chen Jian , Zhang Aijun
Published: May 2018

Benzyl methyl ester, also known as methyl benzoate (MB), is a volatile organic compound that exists naturally as a floral fragrance in many plants. Our behavioral bioassays show that MB and some of its naturally occurring and synthetic analogs kill insects at different life stages. Compared to commercial pesticides containing pyriproxyfen and acetamiprid, MB and some analogs are 1.3 to 3.4 times more toxic to gypsy moth larvae and brown marmorated stinkbug nymphs. The arthropod repellent DEET is also a benzyl ester, and shares the same chemical skeleton with MB. They differ by the diethylamide ester and a methyl group on the benzene ring in DEET. However, unlike MB, DEET does not kill insects; instead, it deters or repels them. Exactly how DEET causes the repellent effect in target organisms is still a mystery. Due to the MB’s structural similarity to DEET, exploring the structure – activity relationship (SAR) of the MB analogs will provide useful information for the discovery of the mode and mechanistic actions of DEET as an insect repellent. In addition, the SAR will allow researchers to modify the chemical structure of the MB molecule, leading to the development of more efficient, safe, and environmentally – friendly green pesticides.
Dependences of microstructure on electromagnetic interference shielding properties of nano-layered Ti3AlC2 ceramics
Authors: Tan Yongqiang , Luo Heng , Zhou Xiaosong , Peng Shuming , Zhang Haibin
Published: May 2018

The microstructure dependent electromagnetic interference (EMI) shielding properties of nano-layered Ti3AlC2ceramics were presented in this study by comparing the shielding properties of various Ti3AlC2ceramics with distinct microstructures. Results indicate that Ti3AlC2ceramics with dense microstructure and coarse grains are more favourable for superior EMI shielding efficiency. High EMI shielding effectiveness over 40 dB at the whole Ku-band frequency range was achieved in Ti3AlC2ceramics by microstructure optimization, and the high shielding effectiveness were well maintained up to 600 °C. A further investigation reveals that only the absorption loss displays variations upon modifying microstructure by allowing more extensive multiple reflections in coarse layered grains. Moreover, the absorption loss of Ti3AlC2was found to be much higher than those of highly conductive TiC ceramics without layered structure. These results demonstrate that nano-layered MAX phase ceramics are promising candidates of high-temperature structural EMI shielding materials and provide insightful suggestions for achieving high EMI shielding efficiency in other ceramic-based shielding materials.
Fabrication of aluminum alloy functionally graded material using directional solidification under an axial static magnetic field
Authors: Hu Shaodong , Gagnoud Annie , Fautrelle Yves , Moreau Rene , Li Xi
Published: May 2018

Aluminum alloy in situ functionally graded materials (FGMs) have been successfully fabricated using directional solidification under an axial static magnetic field. Al-Zn, Al-Ni and Al-Cu alloys with a hypereutectic composition were selected to produce FGMs. Experimental results show that the graded composition of the primary phases (i.e., Zn, Al3Ni and Al2Cu) is obvious along the longitudinal section of the sample. The graded composition of the primary phases could be controlled by the value of the magnetic field, growth rate and temperature gradient. A proposed model and simulations are carried out to explain the origin of the graded composition of the primary phases in FGMs during directional solidification under an axial static magnetic field. It should be attributed to the combined actions of heavier species migration under gravity force and thermoelectric (TE) magnetic convection under magnetic field. Furthermore, it can be found that the magnetic field can induce the columnar FGMs to change into equiaxed FGMs. This work not only presents a new approach to fabricate FGMs using the directional solidification under an axial static magnetic field but also deeply understands the effect of the solute migration and temperature distribution on the crystal growth during directional solidification.
Real-time precise point positioning-based zenith tropospheric delay for precipitation forecasting
Authors: Zhao Qingzhi , Yao Yibin , Yao Wanqiang , Li Zufeng
Published: May 2018

GPS-based Zenith Tropospheric Delay (ZTD) estimation should be easily obtained in a cost-effective way, however, the most previous studies focus on post-processed ZTD estimates using satellite orbit and clock products with at least 3–9 hours latency provided by International GNSS Service (IGS), which limits the GNSS meteorological application for nowcasting. With the development of IGS’s real-time pilot project (RTPP), this limitation was removed by April, 2013 as real-time satellite orbit and clock products can be obtained on-line. In this paper, on the one hand, the GPS-derived ZTD estimation was evaluated using the IGS final and real-time satellite products based on independently developed PPP software. On the other hand, the analysis of the time series of GPS-derived ZTD by least-square fitting of a broken line tendency for a full year of observations, and a forecasting method for precipitation is proposed based on the ZTD slope in the ascending period. The agreement between ZTD slope and the ground rainfall records suggested that the proposed method is useful for the assisted forecasting, especially for short-term alarms.
The live cell DNA stain SiR-Hoechst induces DNA damage responses and impairs cell cycle progression
Authors: Sen Onur , Saurin Adrian T. , Higgins Jonathan M. G.
Published: May 2018

SiR-Hoechst (SiR-DNA) is a far-red fluorescent DNA probe being used widely for time-lapse imaging of living cells that is reported to be minimally toxic at concentrations as high as 10–25 µM. However, measuring nuclear import of Cyclin B1, inhibition of mitotic entry, and the induction of γH2AX foci in cultured human cells reveals that SiR-Hoechst induces DNA damage responses and G2 arrest at concentrations well below 1 µM. SiR-Hoechst is useful for live cell imaging, but it should be used with caution and at the lowest practicable concentration.
Effect of Plant Density, Boron Nutrition and Growth Regulation on Seed Mass, Emergence and Offspring Growth Plasticity in Cotton
Authors: Zohaib Ali , Tabassum Tahira , Jabbar Abdul , Anjum Shakeel Ahmad , Abbas Tasawer , Mehmood Azhar , Irshad Sohail , Kashif Muhammad , Nawaz Mohsin , Farooq Naila , Nasir Irfan Rasool , Rasool Tassadduq , Nadeem Mubashar , Ahmad Riaz
Published: May 2018

Seed nutrients reserves have direct relationship with seed functional traits and influence offspring performance. Effects of plant density, foliage boron (B) nutrition and mepiquat chloride (MC) growth regulation on seed nutrients reserves, seed mass and production, and emergence and offspring growth traits of cotton were studied in two years field experiment. Seed nutrients reserves and seed mass were decreased at higher maternal plant density relative to lower plant density with concomitant decrease in emergence and offspring seedling growth. However, maternal foliage B nutrition and MC growth regulation enhanced seed nutrients reserves, seed mass, emergence and offspring seedling growth performance. There was a significant positive relationship between seed mass and seed nutrients reserves indicating that changes in nutrient availability/uptake in response to maternal ecological factors determine variation in seed functional traits. Nonetheless, seed mass was positively correlated with emergence percentage and negatively with emergence timing. Furthermore, variation in offspring seedling growth traits with seed mass indicated the significance of initial seed nutrients reserves for early seedling vigour and establishment. In conclusion, lower maternal plant density, B nutrition and MC growth regulation ensued in higher emergence and offspring seedling growth of cotton because of higher seed nutrient reserves and seed mass.
Comprehensive analysis of the mouse cytochrome P450 family responsible for omega-3 epoxidation of eicosapentaenoic acid
Authors: Isobe Yosuke , Itagaki Mai , Ito Yuko , Naoe Satoko , Kojima Kotoe , Ikeguchi Mitsunori , Arita Makoto
Published: May 2018

Metabolites generated via oxygenation of the omega-3 double bond (omega-3 oxygenation) in eicosapentaenoic acid (EPA) have recently been identified as novel anti-inflammatory lipid mediators. Therefore, oxygenase(s) responsible for this metabolic pathway are of particular interest. We performed genome-wide screening of mouse cytochrome P450 (CYP) isoforms to explore enzymes involved in omega-3 oxygenation of EPA. As a result, 5 CYP isoforms (mouse Cyp1a2, 2c50, 4a12a, 4a12b, and 4f18) were selected and identified to confer omega-3 epoxidation of EPA to yield 17,18-epoxyeicosatetraenoic acid (17,18-EpETE). Stereoselective production of 17,18-EpETE by each CYP isoform was confirmed, and molecular modeling indicated that chiral differences stem from different EPA binding conformations in the catalytic domains of respective CYP enzymes.
Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota
Authors: Chalermwatanachai Thanit , Vilchez-Vargas Ramiro , Holtappels Gabriele , Lacoere Tim , Jáuregui Ruy , Kerckhof Frederiek-Maarten , Pieper Dietmar H. , Van de Wiele Tom , Vaneechoutte Mario , Van Zele Thibaut , Bachert Claus
Published: May 2018

Chronic rhinosinusitis with nasal polyp (CRSwNP) patients are often characterized by asthma comorbidity and a type-2 inflammation of the sinonasal mucosa. The mucosal microbiota has been suggested to be implicated in the persistence of inflammation, but associations have not been well defined. To compare the bacterial communities of healthy subjects with CRSwNP patients, we collected nasal swabs from 17 healthy subjects, 21 CRSwNP patients without asthma (CRSwNP−A), and 20 CRSwNP patients with co-morbid asthma (CRSwNP+A). We analysed the microbiota using high-throughput sequencing of the bacterial 16S rRNA. Bacterial communities were different between the three groups. Haemophilus influenzae was significantly enriched in CRSwNP patients, Propionibacterium acnes in the healthy group; Staphylococcus aureus was abundant in the CRSwNP−A group, even though present in 57% of patients. Escherichia coli was found in high amounts in CRSwNP+A patients. Nasal tissues of CRSwNP+A patients expressed significantly higher concentrations of IgE, SE-IgE, and IL-5 compared to those of CRSwNP−A patients. Co-cultivation demonstrated that P. acnes growth was inhibited by H. influenzae, E. coli and S. aureus. The nasal microbiota of healthy subjects are different from those of CRSwNP−A and CRSwNP+A patients. However, the most abundant species in healthy status could not inhibit those in CRSwNP disease.
The structural basis of nanobody unfolding reversibility and thermoresistance
Authors: Kunz Patrick , Zinner Katinka , Mücke Norbert , Bartoschik Tanja , Muyldermans Serge , Hoheisel Jörg D.
Published: May 2018

Nanobodies represent the variable binding domain of camelid heavy-chain antibodies and are employed in a rapidly growing range of applications in biotechnology and biomedicine. Their success is based on unique properties including their reported ability to reversibly refold after heat-induced denaturation. This view, however, is contrasted by studies which involve irreversibly aggregating nanobodies, asking for a quantitative analysis that clearly defines nanobody thermoresistance and reveals the determinants of unfolding reversibility and aggregation propensity. By characterizing nearly 70 nanobodies, we show that irreversible aggregation does occur upon heat denaturation for the large majority of binders, potentially affecting application-relevant parameters like stability and immunogenicity. However, by deriving aggregation propensities from apparent melting temperatures, we show that an optional disulfide bond suppresses nanobody aggregation. This effect is further enhanced by increasing the length of a complementarity determining loop which, although expected to destabilize, contributes to nanobody stability. The effect of such variations depends on environmental conditions, however. Nanobodies with two disulfide bonds, for example, are prone to lose their functionality in the cytosol. Our study suggests strategies to engineer nanobodies that exhibit optimal performance parameters and gives insights into general mechanisms which evolved to prevent protein aggregation.
Investigation on the structures and magnetic properties of carbon or nitrogen doped cobalt ferrite nanoparticles
Authors: Cao Derang , Pan Lining , Li Jianan , Cheng Xiaohong , Zhao Zhong , Xu Jie , Li Qiang , Wang Xia , Li Shandong , Wang Jianbo , Liu Qingfang
Published: May 2018

Carbon or nitrogen doped cobalt ferrite nanoparticles were synthesized in the air by a facile calcination process. X-ray diffraction, mapping, X-ray photoelectron spectroscopy, and mössbauer spectra results indicate that the nonmetal elements as the interstitial one are doped into cobalt ferrite nanoparticles. The morphologies of doped cobalt ferrite nanoparticles change from near-spherical to irregular cubelike shapes gradually with the increased carbon or nitrogen concentration, and their particles sizes also increase more than 200 nm. Furthermore, the saturation magnetization of carbon doped cobalt ferrite is improved. Although the saturation magnetization of N-doped cobalt ferrite is not enhanced obviously due to the involved hematite, they also do not drop drastically. The results reveal an approach to synthesize large scale ferrite nanoparticles, and improve the magnetic properties of ferrite nanoparticles, and also provide the potential candidates to synthesis co-doped functional magnetic materials.
Automatic Cone Photoreceptor Localisation in Healthy and Stargardt Afflicted Retinas Using Deep Learning
Authors: Davidson Benjamin , Kalitzeos Angelos , Carroll Joseph , Dubra Alfredo , Ourselin Sebastien , Michaelides Michel , Bergeles Christos
Published: May 2018

We present a robust deep learning framework for the automatic localisation of cone photoreceptor cells in Adaptive Optics Scanning Light Ophthalmoscope (AOSLO) split-detection images. Monitoring cone photoreceptors with AOSLO imaging grants an excellent view into retinal structure and health, provides new perspectives into well known pathologies, and allows clinicians to monitor the effectiveness of experimental treatments. The MultiDimensional Recurrent Neural Network (MDRNN) approach developed in this paper is the first method capable of reliably and automatically identifying cones in both healthy retinas and retinas afflicted with Stargardt disease. Therefore, it represents a leap forward in the computational image processing of AOSLO images, and can provide clinical support in on-going longitudinal studies of disease progression and therapy. We validate our method using images from healthy subjects and subjects with the inherited retinal pathology Stargardt disease, which significantly alters image quality and cone density. We conduct a thorough comparison of our method with current state-of-the-art methods, and demonstrate that the proposed approach is both more accurate and appreciably faster in localizing cones. As further validation to the method’s robustness, we demonstrate it can be successfully applied to images of retinas with pathologies not present in the training data: achromatopsia, and retinitis pigmentosa.
Vanishing river ice cover in the lower part of the Danube basin – signs of a changing climate
Authors: Ionita M. , Badaluta C. -A. , Scholz P. , Chelcea S.
Published: May 2018

Many of the world’s largest rivers in the extra tropics are covered with ice during the cold season, and in the Northern Hemisphere approximately 60% of the rivers experience significant seasonal effects of river ice. Here we present an observational data set of the ice cover regime for the lower part of the Danube River which spans over the period 1837–2016, and its the longest one on record over this area. The results in this study emphasize the strong impact of climate change on the occurrence of ice regime especially in the second part of the 20th century. The number of ice cover days has decreased considerably (~28days/century) mainly due to an increase in the winter mean temperature. In a long-term context, based on documentary evidences, we show that the ice cover occurrence rate was relatively small throughout the Medieval Warm Period (MWP), while the highest occurrence rates were found during the Maunder Minimum and Dalton Minimum periods. We conclude that the river ice regime can be used as a proxy for the winter temperature over the analyzed region and as an indicator of climate-change related impacts.
A multi-phenotypic imaging screen to identify bacterial effectors by exogenous expression in a HeLa cell line
Authors: Collins Adam , Huett Alan
Published: May 2018

We present a high-content screen (HCS) for the simultaneous analysis of multiple phenotypes in HeLa cells expressing an autophagy reporter (mcherry-LC3) and one of 224 GFP-fused proteins from the Crohn’s Disease (CD)-associated bacterium, Adherent Invasive E. coli (AIEC) strain LF82. Using automated confocal microscopy and image analysis (CellProfiler), we localised GFP fusions within cells, and monitored their effects upon autophagy (an important innate cellular defence mechanism), cellular and nuclear morphology, and the actin cytoskeleton. This data will provide an atlas for the localisation of 224 AIEC proteins within human cells, as well as a dataset to analyse their effects upon many aspects of host cell morphology. We also describe an open-source, automated, image-analysis workflow to identify bacterial effectors and their roles via the perturbations induced in reporter cell lines when candidate effectors are exogenously expressed.
A collection of public transport network data sets for 25 cities
Authors: Kujala Rainer , Weckström Christoffer , Darst Richard K. , Mladenović Miloš N , Saramäki Jari
Published: May 2018

Various public transport (PT) agencies publish their route and timetable information with the General Transit Feed Specification (GTFS) as the standard open format. Timetable data are commonly used for PT passenger routing. They can also be used for studying the structure and organization of PT networks, as well as the accessibility and the level of service these networks provide. However, using raw GTFS data is challenging as researchers need to understand the details of the GTFS data format, make sure that the data contain all relevant modes of public transport, and have no errors. To lower the barrier for using GTFS data in research, we publish a curated collection of 25 cities' public transport networks in multiple easy-to-use formats including network edge lists, temporal network event lists, SQLite databases, GeoJSON files, and the GTFS data format. This collection promotes the study of how PT is organized across the globe, and also provides a testbed for developing tools for PT network analysis and PT routing algorithms.
Local symmetry breaking in SnO2 nanocrystals with cobalt doping and its effect on optical properties
Authors: Roy S. , Joshi Amish G. , Chatterjee S. , Ghosh Anup K.
Published: May 2018

Local symmetry breaking in Sn1−xCoxO2 (0.00 ≤ x ≤ 0.04) nanocrystals as evident from Raman spectra (a), and its effect on UV- and green- emissions (b).
Design of Gaussia luciferase-based bioluminescent stem-loop probe for sensitive detection of HIV-1 nucleic acids
Authors: Joda Hamdi , Moutsiopoulou Angeliki , Stone Geoffrey , Daunert Sylvia , Deo Sapna
Published: May 2018

Sensitive detection of HIV-1 nucleic acids using Gaussia luciferase based bioluminescent stem-loop assay.
Immunomodulatory vasoactive intestinal peptide amphiphile micelles
Authors: Zhang Rui , Leeper Caitlin N. , Wang Xiaofei , White Tommi A. , Ulery Bret D.
Published: May 2018

Two different vasoactive intestinal peptide (VIP) amphiphiles have been formulated which readily form micelles of varying shapes. Interestingly, VIP micelle structure has been found to directly correlate to anti-inflammatory behavior providing evidence that these biomaterials can serve as a promising new therapeutic modality.
Production of solar chemicals: gaining selectivity with hybrid molecule/semiconductor assemblies
Authors: Hennessey Seán , Farràs Pau
Published: May 2018

This feature article highlights the use of hybrid molecule/semiconductor devices for the selective production of solar chemicals.
Phonon thermal transport in a class of graphene allotropes from first principles
Authors: Yang Xiuxian , Dai Zhenhong , Zhao Yinchang , Meng Sheng
Published: May 2018

Utilizing first principle calculations combined with the phonon Boltzman transport equation (PBTE), we systematically investigate the phonon thermal transport properties of α, β and γ graphyne, a class of graphene allotropes.
QM/MM studies on ozonolysis of α-humulene and Criegee reactions with acids and water at air–water/acetonitrile interfaces
Authors: Xiao Pin , Yang Jia-Jia , Fang Wei-Hai , Cui Ganglong
Published: May 2018

QM/MM electronic structure calculations reveal important mechanistic insights on the ozonolysis of α-humulene and Criegee reactions with acids and water at air–water/acetonitrile interfaces.
Peptide and protein nanotechnology into the 2020s: beyond biology
Authors: Ulijn Rein V. , Jerala Roman
Published: May 2018

Guest editors Rein Ulijn and Roman Jerala introduce the Peptide and protein nanotechnology themed issue of Chemical Society Reviews.
Brimstone chemistry under laser light assists mass spectrometric detection and imaging the distribution of arsenic in minerals
Authors: Lal Swapnil , Zheng Zhaoyu , Pavlov Julius , Attygalle Athula B.
Published: May 2018

Upon laser irradiation sulfur extracts arsenic from minerals forming AsSn− clusters (n = 2–6) in gas phase.
A hierarchical flower-like hollow alumina supported bimetallic AuPd nanoparticle catalyst for enhanced solvent-free ethylbenzene oxidation
Authors: Dong Huijuan , Xie Renfeng , Yang Lan , Li Feng
Published: May 2018

A hierarchical flower-like hollow alumina supported bimetallic AuPd nanoparticle catalyst exhibited greatly enhanced performance in solvent-free ethylbenzene oxidation.
The structure of urease inactivated by Ag(i): a new paradigm for enzyme inhibition by heavy metals
Authors: Mazzei Luca , Cianci Michele , Gonzalez Vara Antonio , Ciurli Stefano
Published: May 2018

The molecular details of the inactivation of urease, a nickel-dependent virulence factor for human pathogens and negatively affecting the efficiency of soil nitrogen fertilization, are elucidated through the crystal structure of the enzyme complex with Ag(i).