bluuebunny/crossref_metadata_2025 huggingface dataset:
Topological and Non-Topological Solitons in Scalar Field Theories
Authors: Shnir Yakov M.
Published: July 2018

Solitons emerge in various non-linear systems as stable localized configurations, behaving in many ways like particles, from non-linear optics and condensed matter to nuclear physics, cosmology and supersymmetric theories. This book provides an introduction to integrable and non-integrable scalar field models with topological and non-topological soliton solutions. Focusing on both topological and non-topological solitons, it brings together debates around solitary waves and construction of soliton solutions in various models and provides a discussion of solitons using simple model examples. These include the Kortenweg-de-Vries system, sine-Gordon model, kinks and oscillons, and skyrmions and hopfions. The classical field theory of scalar field in various spatial dimensions is used throughout the book in presentation of related concepts, both at the technical and conceptual level. Providing a comprehensive introduction to the description and construction of solitons, this book is ideal for researchers and graduate students in mathematics and theoretical physics.
A. F. “Fred” Spilhaus Jr. (1938–2018)
Authors: Holoviak Judy
Published: July 2018

AGU’s former executive director turned his zeal for defending scientific integrity and for advancing Earth and space research into a 40-year career that enriched scientific pursuits around the world.
Abundance of Light‐Absorbing Anthropogenic Iron Oxide Aerosols in the Urban Atmosphere and Their Emission Sources
Authors: Ohata Sho , Yoshida Atsushi , Moteki Nobuhiro , Adachi Kouji , Takahashi Yoshio , Kurisu Minako , Koike Makoto
Published: July 2018

Light‐absorbing iron oxide (FeOx) aerosols such as magnetite contribute to shortwave atmospheric heating and possibly affect the biogeochemical cycle. However, their atmospheric abundance and emission sources are poorly understood. In this study, we quantified the abundance and mixing states of FeOx at two urban sites in Tokyo and Chiba, Japan, using a modified single‐particle soot photometer and filter‐based instruments. At both sites, the majority of the FeOx were of anthropogenic origin in the form of aggregated magnetite nanoparticles, and their concentrations generally correlated with those of black carbon (BC) and carbon monoxide. In Chiba, where the observatory was located near an integrated steel plant, we observed distinctly high FeOx concentrations and high FeOx/BC concentration ratios when the air mass passed through the plant. From the observed FeOx plumes with the mass equivalent diameter range of 170–2,100 nm, we made an estimate of their emission flux to be approximately 0.012% of the crude steel production, assuming that a Gaussian plume approximation was applicable to our data analysis. Meanwhile, in Tokyo, where the observatory was 20–40 km northwest of steel plants, the FeOx concentrations and FeOx/BC ratios showed clear diurnal variations and depended little on wind direction. This indicates that other human activities also locally produce FeOx aerosols in Tokyo. Our data imply that although steel plant activities emit a large amount of FeOx, emissions from other anthropogenic sources, for example, motor vehicles, have a major contribution to the abundance of FeOx aerosols at the regional and global scales.
Satellite‐Based Daily PM2.5 Estimates During Fire Seasons in Colorado
Authors: Geng Guannan , Murray Nancy L. , Tong Daniel , Fu Joshua S. , Hu Xuefei , Lee Pius , Meng Xia , Chang Howard H. , Liu Yang
Published: July 2018

The western United States has experienced increasing wildfire activities, which have negative effects on human health. Epidemiological studies on fine particulate matter (PM2.5) from wildfires are limited by the lack of accurate high‐resolution PM2.5 exposure data over fire days. Satellite‐based aerosol optical depth (AOD) data can provide additional information in ground PM2.5 concentrations and has been widely used in previous studies. However, the low background concentration, complex terrain, and large wildfire sources add to the challenge of estimating PM2.5 concentrations in the western United States. In this study, we applied a Bayesian ensemble model that combined information from the 1 km resolution AOD products derived from the Multi‐angle Implementation of Atmospheric Correction (MAIAC) algorithm, Community Multiscale Air Quality (CMAQ) model simulations, and ground measurements to predict daily PM2.5 concentrations over fire seasons (April to September) in Colorado for 2011–2014. Our model had a 10‐fold cross‐validated R2 of 0.66 and root‐mean‐squared error of 2.00 μg/m3, outperformed the multistage model, especially on the fire days. Elevated PM2.5 concentrations over large fire events were successfully captured. The modeling technique demonstrated in this study could support future short‐term and long‐term epidemiological studies of wildfire PM2.5.
A Comparison of Cloud Classification Methodologies: Differences Between Cloud and Dynamical Regimes
Authors: McDonald A. J. , Parsons S.
Published: July 2018

Classifications of cloud data into Cloud Regimes (CRs) and compositing based on meteorological parameters, Dynamic Regimes (DRs), are often used in the analysis of clouds. We compare CR and DR classifications to understand the relative merits of these approaches and develop a comparison methodology for future studies. We apply the Self‐Organizing Map technique to International Satellite Cloud Climatology Project (ISCCP) D1 joint histograms to produce a CR and ERA‐Interim pressure vertical velocity output to produce a DR. The CR created improves the separation between high‐level CRs compared to previous work. Composites of ISCCP joint histogram data using the DR produce coherent groupings similar to those in the CR scheme particularly in regions of ascent. Both classifications display coherent geographical patterns and reproduce relationships between vertical velocity and cloud properties. However, the CR produces more coherent clusters with higher intracluster similarity and a greater range of independent cloud classes. Independent tests of composites using ISCCP FD output show that the regional variability of longwave cloud radiative effect for particular nodes are significantly higher in the DR than the CR scheme suggesting a poorer classification. Composite mean CloudSat reflectivity‐altitude joint histograms represent all major cloud types in the CR scheme, while the current DR grouping is less coherent and misses classes. This suggests that the CR scheme is a more useful classification than the DR scheme based solely on vertical velocity data. Contingency table analysis indicates a low association between these classifications, suggesting combining these schemes would be valuable.
Forecasting Rapid Drought Intensification Using the Climate Forecast System (CFS)
Authors: Lorenz D. J. , Otkin J. A. , Svoboda M. , Hain C. R. , Zhong Y.
Published: July 2018

In this study, a statistical method is developed to generate probabilistic forecasts of U.S. Drought Monitor (USDM)‐depicted drought intensification over two‐, four‐, and six‐week time periods using recent observations and forecast model output from the Climate Forecasting System (CFS). The predictors used include weekly anomalies in precipitation, potential evapotranspiration, dew point depression, and soil moisture computed over different time lags. A comparison between the baseline skill obtained using recent observations only and the skill obtained by adding CFS forecast fields as predictors shows that the inclusion of CFS model output leads to only a very modest increase in skill (about 14% increase in variance explained over the central and eastern United States). An analysis of this result reveals that the small increase in skill is due to limited skill in the CFS forecasts themselves, rather than to a time delay in the USDM response to conditions on the ground. Perfect model experiments also show that not all forecast lead times are equally important. For example, in the upper Midwest and western United States, the first two weeks account for at least two thirds of the total realizable skill for a four‐week forecast.
Catchment‐Scale Shifts in the Magnitude and Partitioning of Carbon Export in Response to Changing Hydrologic Connectivity in a Northern Hardwood Forest
Authors: Senar Oscar E. , Webster Kara L. , Creed Irena F.
Published: July 2018

The capacity of forest soils to store organic carbon is influenced by changing hydrologic connectivity. We hypothesized that hydrologic connectivity, the water‐mediated transfer of matter and energy between different landscape positions, controls the partitioning between aquatic and atmospheric soil carbon fates. Results from a 5‐year study of a northern hardwood forested catchment indicated that hydrologic connectivity affected both the magnitude and fate of carbon export. Atmospheric carbon export was the major export pathway from the catchment; its rate was regulated by topographic position (i.e., uplands, ecotones, and wetlands) but enhanced or supressed through changes in soil moisture and hydrologic connectivity. Wetter soil conditions reduced CO2 flux from the ecotones and wetlands where microbial respiration was oxygen‐limited, whereas drier soil conditions that decreased hydrologic connectivity increased CO2 flux by relieving the oxygen limitation. In contrast, aquatic carbon export was a minor export pathway from the catchment and was driven by hydrologic connectivity, with less carbon export during relatively low discharge years. Past trends suggest a shift to a warmer climate and changes in the timing, duration, and intensity of hydrologic connectivity that are leading to an increase in annual atmospheric carbon export but a decrease in annual aquatic carbon export, despite the intensification of autumn storms. The increase in atmospheric carbon export creates a positive feedback for climate warming that will further disrupt hydrologic connectivity and aquatic carbon export, with consequences for downstream streams and lakes.
Adding Depth to Our Understanding of Nitrogen Dynamics in Permafrost Soils
Authors: Salmon Verity G. , Schädel Christina , Bracho Rosvel , Pegoraro Elaine , Celis Gerardo , Mauritz Marguerite , Mack Michelle C. , Schuur Edward A. G.
Published: July 2018

Losses of C from decomposing permafrost may be offset by increased productivity of tundra plants, but nitrogen availability partially limits plant growth in tundra ecosystems. In this soil incubation experiment carbon (C) and nitrogen (N) cycling dynamics were examined from the soil surface down through upper permafrost. We found that losses of CO2were negatively correlated to net N mineralization because C‐rich surface soils mineralized little N, while deep soils had low rates of C respiration but high rates of net N mineralization. Permafrost soils released a large flush of inorganic N when initially thawed. Depth‐specific rates of N mineralization from the incubation were combined with thaw depths and soil temperatures from a nearby manipulative warming experiment to simulate the potential magnitude, timing, and depth of inorganic N release during the process of permafrost thaw. Our calculations show that inorganic N released from newly thawed permafrost may be similar in magnitude to the increase in N mineralized by warmed soils in the middle of the profile. The total release of inorganic N from the soil profile during the simulated thaw process was twice the size of the observed increase in the foliar N pool observed at the manipulative experiment. Our findings suggest that increases in N availability are likely to outpace the N demand of tundra plants during the first 5 years of permafrost thaw and may increase C losses from surface soils as well as induce denitrification and leaching of N from these ecosystems.
What Is the Range of Soil Water Density? Critical Reviews With a Unified Model
Authors: Zhang Chao , Lu Ning
Published: July 2018

The soil water density is defined as the ratio of soil water mass to soil water volume. It is a cornerstone in defining thermodynamic states of either saturated or unsaturated soils for quantifying water storage and movement in the subsurface and for mechanical stability of landscape. So far, it has been widely treated as identical to the free water density, that is, a constant of 0.997 g/cm3, but can be remarkably different from this value as it is subject to a wide range of variation in energy levels. Some experimental and theoretical evidence indicate that it can be as high as 1.680 g/cm3 and as low as 0.752 g/cm3. However, to date, there is no unanimous agreement upon a reliable experimental method to measure the soil water density or a unified theory to explain why and how the soil water density can deviate remarkably from the free water density. Consequently, the understanding of the soil water density is controversial and elusive, or some theories are contradictory to each other. In this review, the authors will (1) conduct critical reviews on the experimental and theoretical methodologies to identify their limitations, flaws, and uncertainties, (2) synthesize some recent findings on intermolecular forces, interfacial interactions, and soil water retention mechanisms to clarify molecular‐scale physicochemical mechanisms governing the soil water density, and (3) propose a unified model to quantify soil water density variation. It is found that capillarity associated with surface tension tends to generate tensile stress in soil water and thereby decreases the soil water density, whereas adsorption stemmed from cation hydration, surface hydration, and interlamellar cation hydration tends to produce compressive stress thus increases the soil water density. Furthermore, the abnormally high water density greater than 1.15 g/cm3 is a result of cation and surface hydration that involves significant water structure change around exchangeable cations and mineral surface hydroxyls. The unified soil water density model, explicitly quantifying adsorptive and capillary water, could potentially reconcile the unresolved controversies. The critical reviews and the unified model also would allow us to further confine the upper and lower bounds of the soil water density. The upper bound is theoretically inferred to be around 1.872 g/cm3, whereas the lower bound is around 0.995 g/cm3; both are higher than that reported in the literature. With the unified model and measured soil water retention curves, it is demonstrated quantitatively that the soil water density significantly impacts the magnitude of various fundamental soil properties such as matric potential, specific surface area, and volumetric water content. The abnormally high soil water density has significant implications to the conventional concepts of matric potential and pore water pressure in soils and other earthen porous materials.
Synthesis of nylon 1 in supercritical carbon dioxide and its crystallization behavior effect on nylon 11
Authors: Yuan Dandan , Bao Jianxu , Ren Ying , Li Wenmin , Huang Lei , Cai Xufu
Published: July 2018

Nylon-1, with the highest density of dipoles among odd-numbered nylons, was synthesized through urea in supercritical CO2.
A chiral spiroborate anion from diphenyl-l-tartramide [B{l-Tar(NHPh)2}2]−applied to some challenging resolutions
Authors: Wong Lawrence W.-Y. , Tam Gemma S.-S. , Chen Xiaoyan , So Frederick T.-K. , Soecipto Aristyo , Sheong Fu Kit , Sung Herman H.-Y. , Lin Zhenyang , Williams Ian D.
Published: July 2018

A chiral spiroborate anion [B{l-Tar(NHPh)2}2]−is effective in challenging high yield, 1-pot resolutions, as for the S-2-phenylpropylammonium salt shown.
Thermal processing of zeolite seed layers for the fabrication of compact oriented MFI zeolite films
Authors: Peng Yong , Xu Ruilan , Jiang Xinde , Xu Sheng , Wang Zhengbao
Published: July 2018

The formation of a close-packed oriented MFI zeolite film through thermal processing created a strong covalent linkage between the seed layer and the substrate.
Overwhelming coexistence of negative differential resistance effect and RRAM
Authors: Guo Tao , Sun Bai , Zhou Yu , Zhao Hongbin , Lei Ming , Zhao Yong
Published: July 2018

An overwhelming coexistence of NDR effect and RS memory behavior at room temperature was observed based on Ag/CZTSe/Mo devices.
Substituted troponimines: when aromatization of the conjugate acid leads to very strong neutral organic superbases
Authors: Saadat Kayvan , Shiri Ali , Kovačević Borislav
Published: July 2018

Highly basic 3,6-disubstituted troponimino-scaffolds enable the introduction of new aromatic-stabilizing neutral organic superbase groups.
An efficient and stable narrow band Mn4+-activated fluorotitanate red phosphor Rb2TiF6:Mn4+ for warm white LED applications
Authors: Wang L. Y. , Song E. H. , Zhou Y. Y. , Deng T. T. , Ye S. , Zhang Q. Y.
Published: July 2018

A Rb-based fluorotitanate red-emitting phosphor Rb2TiF6:MnM4+ with an internal quantum efficiency of 91% was synthesized and presents exceptional luminescence properties, thermal stability and longevity under LED working conditions.
Mechanisms of tooth damage and Paranthropus dietary reconstruction
Authors: Constantino Paul Joseph , Borrero‐Lopez Oscar , Lawn Brian R.
Published: July 2018

According to the current fossil record, the extinct hominin genus Paranthropus and the genus Homo both first appeared ∼2.7 million years ago. Despite this similarity in geological age, Paranthropus evolved enormous postcanine teeth with very thick enamel while Homo evolved smaller teeth. Results from contact mechanics models derived from multiple scales of tooth damage (microwear, macrowear, and fracture) are reviewed to examine this evolutionary divergence and the role that diet may have played in it. Each scale of investigation reveals different kinds of evidence that can be combined into a more complete picture of hominin diet and feeding behaviour. Microwear reveals information about recent feeding events, while macrowear and fracture record longer‐term trends. The synthesis of all three levels of evidence exposes significant dietary diversity, not only between these two hominin genera but within them as well. Within Paranthropus, the eastern and southern African species (P. boisei and P. robustus, respectively) were morphologically similar but appear to have been functionally different. Whereas P. boisei apparently used its teeth to consume large quantities of low quality vegetation, P. robustus had a more varied diet that included harder objects, possibly items such as seeds, nuts, or underground storage organs.
Determination of the power transmission line ageing failure probability due to the impact of forest fire
Authors: Guo Yufeng , Chen Runxin , Shi Jianguo , Wan Jie , Yi Hongliang , Zhong Jin
Published: July 2018

With increased occurrences of a forest fire, the short‐term reliability of power transmission lines needs to be re‐evaluated considering the impact of forest fire on the ageing of transmission lines. How to include the impacts from a forest fire on line ageing in a comprehensive way becomes an important issue for the study of line failure probability. In this study, a method is proposed to evaluate the impact of forest fire on line ageing degree based on dynamic heat balance equation and Weibull distribution. The method will help maintenance staffs to assess the damage level of transmission lines. The method is tested by a contrast experiment and a case study with real meteorological data. Simulation results show that forest fire can greatly threaten the reliability of power transmission lines, while during this process flame characteristics, wind and load ratio could be the major factors that affect the line reliability. With the results obtained, this study also provides the system operator with valuable instructions on how to reduce the damages caused by fire to transmission lines.
Antenna design using dynamic multi‐objective evolutionary algorithm
Authors: Jiao Ruwang , Sun Yongzhi , Sun Jianqing , Jiang Yuhong , Zeng Sanyou
Published: July 2018

To enhance the robustness and stability of the antenna design, a novel methodology is presented for modelling the antenna design problem as the constrained optimisation problem (COP). Then a framework is introduced for solving the COP. The framework converts a COP into an equivalent dynamic constrained multi‐objective optimisation problem (DCMOP). A dynamic constrained multi‐objective evolutionary algorithm is applied to address the transformed DCMOP, which means the COP as well as the antenna design problem can be solved. Then it is applied to design three classes of antennas: a wire antenna, a patch antenna and an antenna array. Obtained results of these three kinds of antenna suggest that the proposed methods can well satisfy the antenna design requirements.
Designing steel to resist hydrogen embrittlement: Part 1 – trapping capacity
Authors: Ramjaun T. I. , Ooi S. W. , Morana R. , Bhadeshia H. K. D. H.
Published: July 2018

A novel steel has been designed for use in the oil and gas industry, displaying properties comparable with the currently available F22 grade and possessing the additional quality of excellent hydrogen trapping capacity. Its high strength is derived from a martensitic microstructure containing a dispersion of fine vanadium-molybdenum carbides that evolve during thermal treatments. If the tempering cycle is controlled such that the precipitates maintain a degree of coherency with the matrix, then they act as hydrogen trapping sites, due to the associated strain fields, thus mitigating the problem of diffusible hydrogen. Using material modelling programmes and small-scale sample alloys this work describes the process of the new steel design and demonstrates its superior trapping capacity through thermal desorption analysis.
Designing steel to resist hydrogen embrittlement Part 2 – precipitate characterisation
Authors: Ooi S. W. , Ramjaun T. I. , Hulme-Smith C. , Morana R. , Drakopoulos M. , Bhadeshia H. K. D. H.
Published: July 2018

A novel, low-alloy steel has been designed for use in the oil and gas industry. Its high strength and hydrogen trapping potential are derived from a martensitic microstructure containing a dispersion of fine vanadium–molybdenum alloy carbides that evolve during tempering. In this second paper, the effect of quench rate from austenitisation and tempering conditions are investigated with respect to the microstructure. The alloy loses its tempering resistance following slow-cooling from austenitisation as a result of MC precipitation, leading to vanadium depletion and significant M[Formula: see text]C coarsening. This is predicted using computer simulation and confirmed by high energy X-ray diffraction, combined with electron microscopy.
Alternative assessment of knee joint muscle balance of soccer players through total work‐based hamstring: quadriceps ratios
Authors: Minozzo Felipe , Lopez Pedro , Machado Carlos Leonardo Figueiredo , Wilhelm Eurico Nestor , Grazioli Rafael , Pinto Ronei Silveira
Published: July 2018

Isokinetic hamstring‐to‐quadriceps (H:Q) ratios are frequently used to assess knee muscle strength imbalances and risk of injuries/re‐injuries. The use of peak torque (PT) or total work (TW) to estimate joint stability may lead to different results because of the differences between these two neuromuscular variables. Thus, the current study aimed to compare the conventional and functional H:Q ratios calculated by PT and TW. Ninety‐three male professional soccer players from Brazilian first division teams performed isokinetic concentric and eccentric contractions of the quadriceps and the hamstrings at 60°/s. Muscle strength balance was calculated using the conventional torque ratio (CTR) and conventional work ratio (CWR), functional torque ratio (FTR) and functional work ratio (FWR) were highly and moderately correlated between them (r = 0.83 and r = 0.73, respectively). The Wilcoxon statistical test revealed significant differences between CTR and CWR, as well as FTR and FWR (p < 0.05). T‐test demonstrated significant differences in mean CTR–CWR and FTR–FWR, whereas Bland–Altman plots showed non‐consistent bias. In addition, the chi‐square test demonstrated significant differences between players below the conventional reference values and functional reference values (p < 0.001). In conclusion, TW ratios seem to provide distinct and additional information regarding the H:Q strength balance in professional soccer players. Moreover, taking into account that TW captures torque information throughout the entire range of motion, it is possible that TW ratios represent a more comprehensive assessment of muscle strength imbalance.
What Is the Use Value of Irrigation Water from the High Plains Aquifer?
Authors: García Suárez Federico , Fulginiti Lilyan E. , Perrin Richard K.
Published: July 2018

This study provides an estimate of the gross value of irrigation water from the U.S. High Plains Aquifer. We estimate a yield function for aggregated crop biomass production, based on county‐level observations for 1960–2007. This study found that irrigation increases total biomass yield in this region by an average of 51%. We estimate the average gross annual value of irrigation as of 2007 to be $196 per acre, for a total of about $3 billion across the aquifer. We also estimate that on average across the aquifer, exposure to 24 hours of temperatures above 33°C (one degree day) reduces biomass yield by 3%, with a value in 2007 of about $10 per acre.
Increased Resting Heart Rate on Electrocardiogram Relative to In-office Pulse Rate Indicates Cardiac Overload: The J-HOP Study
Authors: Oba Yusuke , Hoshide Satoshi , Kabutoya Tomoyuki , Kario Kazuomi
Published: July 2018

BACKGROUND

Heart rate (HR) assessed by electrocardiogram (ECG-HR) and pulse rate (PR) measured in a physician’s office (office-PR) are taken with subjects in different body positions—i.e., supine vs. sitting. Although analysis of HR differences according to body position could provide new practical insights, there have been few studies on the subject. We herein investigated whether the difference between office-PR and ECG-HR (delta HR) was associated with brain natriuretic peptide (BNP) levels and left ventricular mass (LVM).

METHODS

Among the 4,310 patients with 1 or more cardiovascular risk factors recruited for the Japan Morning Surge-Home Blood Pressure study, we excluded those with atrial fibrillation or a prescribed β-blocker. We analyzed the 2,972 patients who had ECG-HR, office-PR, and BNP data and 1,061 patients with echocardiography data.

RESULTS

In the complete patient series, office-PR was significantly higher than ECG-HR (72.1 ± 10.3 vs. 66.6 ± 11.9 bpm, P < 0.001). When we divided patients into quintiles based on the delta HR, the BNP level and LVM index (LVMI) decreased across categories after adjustment for traditional cardiovascular risk factors (each P ≤ 0.001). In a multiple linear regression analysis, the delta HR was independently and significantly associated with both the log-transformed BNP level (β = −0.179, P < 0.001) and LVMI (β = −0.113, P = 0.001) adjusted for covariates.

CONCLUSION

A decreased delta HR was positively associated with the BNP level and LVMI. Without the requirement of a special technique, this evaluation might indicate potential cardiac overload and provide a clinical sign related to heart failure.
Differential Associations of Diastolic and Systolic Pressures With Cerebral Measures in Older Individuals With Mild Cognitive Impairment
Authors: Shokouhi Mahsa , Qiu Deqiang , Samman Tahhan Ayman , Quyyumi Arshed A , Hajjar Ihab
Published: July 2018

BACKGROUND

Reports on the relative importance of the diastolic and systolic blood pressures (DBP and SBP) in age-related cognitive decline are mixed. Investigating the relation between DBP/SBP and functional and structural brain changes could elucidate which of the 2 measures is more critically important for brain function and, consequently, cognitive impairment.

METHODS

We investigated the association of SBP and DBP with cortical volume, cerebral blood flow (CBF), and white matter lesions (WML), in nondemented older adults with and without mild cognitive impairment (MCI; N = 265, 185 MCI, mean age = 64 years). Brachial blood pressure was measured twice while seated, and the average of the 2 measures was used. Cortical volume, gray matter (GM) CBF, and WML were estimated using T1-weighted imaging, arterial spin labeling, and fluid attenuation inversion recovery, respectively.

RESULTS

Reduced cortical volume was associated with elevated DBP (β= −0.18, P = 0.034) but not with SBP (β = −0.10, P = 0.206). GM CBF was associated with DBP (β = −0.13, P = 0.048) but not with SBP (β = −0.07, P = 0.275). Likewise, CBF within brain regions where MCI patients showed hypoperfusion were only associated with DBP (DBP: β = −0.17, P = 0.005; SBP: β = −0.09, P = 0.120). WML volume was associated with both DBP (β = 0.20, P = 0.005) and SBP (β = 0.30, P < 0.001). For all measures, there was no interaction between DBP/SBP and cognitive status, indicating that these associations were independent of the cognitive status.

CONCLUSIONS

Independently of the cognitive status, DBP is more critically important for GM volume and perfusion, whereas WML is associated with both blood pressures, likely reflecting long-term effect of hypertension and autoregulation dysfunction.
Black–White Difference in the Impact of Long-Term Blood Pressure From Childhood on Adult Renal Function: The Bogalusa Heart Study
Authors: Yan Yinkun , Zhang Tao , Li Shengxu , Liu Yang , Bazzano Lydia , He Jiang , Mi Jie , Chen Wei
Published: July 2018

BACKGROUND

To examine racial difference in the impact of long-term burden of blood pressure (BP) from childhood on adult renal function between middle-aged blacks and whites.

METHODS

The study cohort consisted of 1,646 whites and 866 blacks aged 20–51 years at follow-up who had BP measured at least 4 times since childhood, with a mean follow-up period of 25.3 years. The area under the curve (AUC) was calculated as a measure of long-term burden of BP from childhood to adulthood. Estimated glomerular filtration rate (eGFR) was calculated based on serum creatinine to assess renal function in adulthood.

RESULTS

Black vs. white adults had significantly higher values of eGFR and long-term burden of systolic BP for both males and females. In multivariable linear regression analyses, adjusting for sex, adult age, body mass index, smoking, and alcohol use, adult eGFR was significantly and negatively associated with adult systolic BP (standardized regression coefficient [β] = −0.10, P = 0.005) and diastolic BP (β = −0.11, P = 0.003) in blacks, but not in whites. The total BP AUC values were also significantly and negatively associated with adult eGFR (β = −0.10, P = 0.005 for systolic BP and β = −0.09, P = 0.013 for diastolic BP) in blacks only. Childhood BP was not significantly associated with adult eGFR in blacks and whites.

CONCLUSIONS

These findings suggest that black–white disparities in the influence of elevated BP on the development of renal dysfunction occur in middle adulthood, which underscores the importance of BP control in the black population.
Review and comparative assessment of similarity-based methods for prediction of drug–protein interactions in the druggable human proteome
Authors: Wang Chen , Kurgan Lukasz
Published: July 2018

Drug–protein interactions (DPIs) underlie the desired therapeutic actions and the adverse side effects of a significant majority of drugs. Computational prediction of DPIs facilitates research in drug discovery, characterization and repurposing. Similarity-based methods that do not require knowledge of protein structures are particularly suitable for druggable genome-wide predictions of DPIs. We review 35 high-impact similarity-based predictors that were published in the past decade. We group them based on three types of similarities and their combinations that they use. We discuss and compare key aspects of these methods including source databases, internal databases and their predictive models. Using our novel benchmark database, we perform comparative empirical analysis of predictive performance of seven types of representative predictors that utilize each type of similarity individually and all possible combinations of similarities. We assess predictive quality at the database-wide DPI level and we are the first to also include evaluation over individual drugs. Our comprehensive analysis shows that predictors that use more similarity types outperform methods that employ fewer similarities, and that the model combining all three types of similarities secures area under the receiver operating characteristic curve of 0.93. We offer a comprehensive analysis of sensitivity of predictive performance to intrinsic and extrinsic characteristics of the considered predictors. We find that predictive performance is sensitive to low levels of similarities between sequences of the drug targets and several extrinsic properties of the input drug structures, drug profiles and drug targets. The benchmark database and a webserver for the seven predictors are freely available at http://biomine.cs.vcu.edu/servers/CONNECTOR/.
Comprehensive comparative analysis of methods and software for identifying viral integrations
Authors: Chen Xun , Kost Jason , Li Dawei
Published: July 2018

Many viruses are capable of integrating in the human genome, particularly viruses involved in tumorigenesis. Viral integrations can be considered genetic markers for discovering virus-caused cancers and inferring cancer cell development. Next-generation sequencing (NGS) technologies have been widely used to screen for viral integrations in cancer genomes, and a number of bioinformatics tools have been developed to detect viral integrations using NGS data. However, there has been no systematic comparison of the methods or software. In this study, we performed a comprehensive comparative analysis of the designs, performance, functionality and limitations among the existing methods and software for detecting viral integrations. We further compared the sensitivity, precision and runtime of integration detection of four representative tools. Our analyses showed that each of the existing software had its own merits; however, none of them were sufficient for parallel or accurate virome-wide detection. After carefully evaluating the limitations shared by the existing methods, we proposed strategies and directions for developing virome-wide integration detection.
Insights on the alteration of functionality of a tyrosine kinase 2 variant: a molecular dynamics study
Authors: Lesgidou Nastazia , Eliopoulos Elias , Goulielmos George N , Vlassi Metaxia
Published: July 2018

Motivation

The tyrosine kinase 2 protein (Tyk2), encoded by the TYK2 gene, has a crucial role in signal transduction and the pathogenesis of many diseases. A single nucleotide polymorphism of the TYK2 gene, SNP rs34536443, is of major importance, since it has been shown to confer protection against various, mainly, autoimmune diseases. This polymorphism results in a Pro to Ala change at amino acid position 1104 of the encoded Tyk2 protein that affects its enzymatic activity. However, the details of the underlined mechanism are unknown. To address this issue, in this study, we used molecular dynamics simulations on the kinase domains of both wild type and variant Tyk2 protein.

Results

Our MD results provided information, at atomic level, on the consequences of the Pro1104 to Ala substitution on the structure and dynamics of the kinase domain of Tyk2 and suggested reduced enzymatic activity of the resulting protein variant due to stabilization of inactive conformations, thus adding to knowledge towards the elucidation of the protection mechanism against autoimmune diseases associated with this point mutation.
MAVIS: merging, annotation, validation, and illustration of structural variants
Authors: Reisle Caralyn , Mungall Karen L , Choo Caleb , Paulino Daniel , Bleile Dustin W , Muhammadzadeh Amir , Mungall Andrew J , Moore Richard A , Shlafman Inna , Coope Robin , Pleasance Stephen , Ma Yussanne , Jones Steven J M
Published: July 2018

Reliably identifying genomic rearrangements and interpreting their impact is a key step in understanding their role in human cancers and inherited genetic diseases. Many short read algorithmic approaches exist but all have appreciable false negative rates. A common approach is to evaluate the union of multiple tools increasing sensitivity, followed by filtering to retain specificity. Here we describe an application framework for the rapid generation of structural variant consensus, unique in its ability to visualize the genetic impact and context as well as process both genome and transcriptome data.

Availability and implementation

http://mavis.bcgsc.ca

Supplementary information

Supplementary data are available at Bioinformatics online.
Reproducible and replicable comparisons using SummarizedBenchmark
Authors: Kimes Patrick K , Reyes Alejandro
Published: July 2018

Benchmark studies are widely used to compare and evaluate tools developed for answering various biological questions. Despite the popularity of these comparisons, the implementation is often ad hoc, with little consistency across studies. To address this problem, we developed SummarizedBenchmark, an R package and framework for organizing and structuring benchmark comparisons. SummarizedBenchmark defines a general grammar for benchmarking and allows for easier setup and execution of benchmark comparisons, while improving the reproducibility and replicability of such comparisons. We demonstrate the wide applicability of our framework using four examples from different applications.

Availability and implementation

SummarizedBenchmark is an R package available through Bioconductor (http://bioconductor.org/packages/SummarizedBenchmark).

Supplementary information

Supplementary data are available at Bioinformatics online.
Simulating Illumina metagenomic data with InSilicoSeq
Authors: Gourlé Hadrien , Karlsson-Lindsjö Oskar , Hayer Juliette , Bongcam-Rudloff Erik
Published: July 2018

Motivation

The accurate in silico simulation of metagenomic datasets is of great importance for benchmarking bioinformatics tools as well as for experimental design. Users are dependant on large-scale simulation to not only design experiments and new projects but also for accurate estimation of computational needs within a project. Unfortunately, most current read simulators are either not suited for metagenomics, out of date or relatively poorly documented. In this article, we describe InSilicoSeq, a software package to simulate metagenomic Illumina sequencing data. InsilicoSeq has a simple command-line interface and extensive documentation.

Results

InSilicoSeq is implemented in Python and capable of simulating realistic Illumina (meta) genomic data in a parallel fashion with sensible default parameters.

Availability and implementation

Source code and documentation are available under the MIT license at https://github.com/HadrienG/InSilicoSeq and https://insilicoseq.readthedocs.io/.

Supplementary information

Supplementary data are available at Bioinformatics online.
SonicParanoid: fast, accurate and easy orthology inference
Authors: Cosentino Salvatore , Iwasaki Wataru
Published: July 2018

Motivation

Orthology inference constitutes a common base of many genome-based studies, as a pre-requisite for annotating new genomes, finding target genes for biotechnological applications and revealing the evolutionary history of life. Although its importance keeps rising with the ever-growing number of sequenced genomes, existing tools are computationally demanding and difficult to employ.

Results

Here, we present SonicParanoid, which is faster than, but comparably accurate to, the well-established tools with a balanced precision-recall trade-off. Furthermore, SonicParanoid substantially relieves the difficulties of orthology inference for those who need to construct and maintain their own genomic datasets.

Availability and implementation

SonicParanoid is available with a GNU GPLv3 license on the Python Package Index and BitBucket. Documentation is available at http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid.

Supplementary information

Supplementary data are available at Bioinformatics online.
Being a good egg in the 21st century
Authors: Anderson Richard A , Telfer Evelyn E
Published: July 2018

Introduction

Women are increasingly having children at a later age, but this can conflict with declining fertility in the later 30′s and thereafter.

Areas of agreement

Declining egg quality and quantity with age are well-established, although egg quality can only be surmised from reproductive success or failure.

Areas of controversy

Whether increasing the number of eggs that can be obtained from ovarian stimulation is of value, and whether there are precursor cells within the adult ovary that could become mature eggs.

Growing points

There is increasing use of donated eggs by older women to enhance their chances of conception. The storage of frozen eggs for potential use later in life is also becoming more common.

Areas timely for developing research

Understanding of growth initiation of follicles and development of an artificial ovary may lead to the ability to affect fertility and reproductive lifespan.
Legitimating Media: Shakespeare’s Awkward Travels Through Video Games and Twitter
Authors: Cornfeld Li , Simon Victoria , Sterne Jonathan
Published: July 2018

Since the 19th century, Shakespeare references have recurred with surprising consistency in experimental forms of media. This article considers the role of references to and adaptations of Shakespeare texts when a media form takes on a new valence for a set of users in a particular time and place. We consider two different moments at length: a commercial interactive game from 1984 that made novel use of cassettes and sound, and the production and reception of early Twitter adaptations of Shakespeare in 2010. By standing in for the aesthetic possibilities and limits of a changing media space, Shakespearean references and deviations from them serve a key role for artists and critics in debates over the legitimacy and significance of creative work in emergent media. Thus, cultural producers, critics and audiences thus use these sometimes-awkward appearances of Shakespeare as a means of describing their aesthetic potentials and limits.
Maintained Frontal Activity Underlies High Memory Function Over 8 Years in Aging
Authors: Vidal-Piñeiro Didac , Sneve Markus H , Nyberg Lars H , Mowinckel Athanasia M , Sederevicius Donatas , Walhovd Kristine B , Fjell Anders M
Published: July 2018

Aging is characterized by substantial average decline in memory performance. Yet contradictory explanations have been given for how the brains of high-performing older adults work: either by engagement of compensatory processes such as recruitment of additional networks or by maintaining young adults’ patterns of activity. Distinguishing these components requires large experimental samples and longitudinal follow-up. Here, we investigate which features are key to high memory in aging, directly testing these hypotheses by studying a large sample of adult participants (n > 300) with fMRI during an episodic memory experiment where item-context relationships were implicitly encoded. The analyses revealed that low levels of activity in frontal networks—known to be involved in memory encoding—were associated with low memory performance in the older adults only. Importantly, older participants with low memory performance and low frontal activity exhibited a strong longitudinal memory decline in an independent verbal episodic memory task spanning 8 years back (n = 52). These participants were also characterized by lower hippocampal volumes and steeper rates of cortical atrophy. Altogether, maintenance of frontal brain function during encoding seems to be a primary characteristic of preservation of memory function in aging, likely reflecting intact ability to integrate information.
Adolescent Nicotine Exposure Induces Dysregulation of Mesocorticolimbic Activity States and Depressive and Anxiety-like Prefrontal Cortical Molecular Phenotypes Persisting into Adulthood
Authors: Jobson Christina L M , Renard Justine , Szkudlarek Hanna , Rosen Laura G , Pereira Brian , Wright Daniel J , Rushlow Walter , Laviolette Steven R
Published: July 2018

Considerable evidence demonstrates strong comorbidity between nicotine dependence and mood and anxiety disorders. Nevertheless, the neurobiological mechanisms linking adolescent nicotine exposure to mood and anxiety disorders are not known. Disturbances in the mesocorticolimbic dopamine (DA) system, comprising the prefrontal cortex (PFC), ventral tegmental area (VTA), and nucleus accumbens (NAc), are correlates of mood and anxiety-related symptoms and this circuitry is strongly influenced by acute or chronic nicotine exposure. Using a combination of behavioral pharmacology, in vivo neuronal electrophysiology and molecular analyses, we examined and compared the effects of chronic nicotine exposure in rats during adolescence versus adulthood to characterize the mechanisms by which adolescent nicotine may selectively confer increased risk of developing mood and anxiety-related symptoms in later life. We report that exposure to nicotine, selectively during adolescence, induces profound and long-lasting neuronal, molecular and behavioral disturbances involving PFC DA D1R and downstream extracellular-signal-related kinase 1-2 (ERK 1-2) signaling. Remarkably, adolescent nicotine induced a persistent state of hyperactive DA activity in the ventral tegmental area (VTA) concomitant with hyperactive neuronal activity states in the PFC. Our findings identify several unique neuronal and molecular biomarkers that may serve as functional risk mechanisms for the long-lasting neuropsychiatric effects of adolescent smoking behaviors.
Reappraisal of Interpersonal Criticism in Social Anxiety Disorder: A Brain Network Hierarchy Perspective
Authors: Jacob Y , Shany O , Goldin P R , Gross J J , Hendler T
Published: July 2018

Emotion regulation is thought to involve communication between and within large-scale brain networks that underlie emotion reactivity and cognitive control. Aberrant network interaction might therefore be a key neural feature of mental disorders that involve emotion dysregulation. Here we tested whether connectivity hierarchies within and between emotion reactivity and cognitive reappraisal networks distinguishes social anxiety disorder (SAD) patients (n = 70) from healthy controls (HC) (n = 25). To investigate network organization, we implemented a graph-theory method called Dependency Network Analysis. Participants underwent fMRI while watching or reappraising video clips involving interpersonal verbal criticism. During reappraisal, the reappraisal network exerted less influence on the reactivity network in SAD participants. Specifically, the influence of the right inferior frontal gyrus on both reappraisal and reactivity networks was significantly reduced in SAD compared with HC, and correlated negatively with negative emotion ratings among SAD participants. Surprisingly, the amygdala exhibited reduced influence on the reappraisal network in SAD relative to HC. Yet, during the watch condition, the left amygdala’s influence on the reactivity network increased with greater social anxiety symptoms among SAD participants. These findings refine our understanding of network organization that contributes to efficient reappraisal or to disturbances in applying this strategy in SAD.