bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noninvasive Continuous Monitoring of Adipocyte Differentiation: From Macro to Micro Scales
Authors: Lustig Maayan , Feng Qingling , Payan Yohan , Gefen Amit , Benayahu Dafna 
Published: February 2019

Abstract3T3-L1 cells serve as model systems for studying adipogenesis and research of adipose tissue-related diseases, e.g. obesity and diabetes. Here, we present two novel and complementary nondestructive methods for adipogenesis analysis of living cells which facilitate continuous monitoring of the same culture over extended periods of time, and are applied in parallel at the macro- and micro-scales. At the macro-scale, we developed visual differences mapping (VDM), a novel method which allows to determine level of adipogenesis (LOA)—a numerical index which quantitatively describes the extent of differentiation in the whole culture, and percentage area populated by adipocytes (PAPBA) across a whole culture, based on the apparent morphological differences between preadipocytes and adipocytes. At the micro-scale, we developed an improved version of our previously published image-processing algorithm, which now provides data regarding single-cell morphology and lipid contents. Both methods were applied here synergistically for measuring differentiation levels in cultures over multiple weeks. VDM revealed that the mean LOA value reached 1.11 ± 0.06 and the mean PAPBA value reached >60%. Micro-scale analysis revealed that during differentiation, the cells transformed from a fibroblast-like shape to a circular shape with a build-up of lipid droplets. We predict a vast potential for implementation of these methods in adipose-related pharmacological research, such as in metabolic-syndrome studies.
CD81 Promotes a Migratory Phenotype in Neuronal-Like Cells
Authors: Martins Soraia A. , Correia Patrícia D. , Dias Roberto A. , da Cruz e Silva Odete A.B. , Vieira Sandra I. 
Published: February 2019

AbstractTetraspanins, such as CD81, can form lateral associations with each other and with other transmembrane proteins. These interactions may underlie CD81 functions in multiple cellular processes, such as adhesion, morphology, migration, and differentiation. Since CD81's role in neuronal cells’ migration has not been established, we here evaluated effects of CD81 on the migratory phenotype of SH-SY5Y neuroblastoma cells. CD81 was found enriched at SH-SY5Y cell's membrane, co-localizing with its interactor filamentous-actin (F-actin) in migratory relevant structures of the leading edge (filopodia, stress fibers, and adhesion sites). CD81 overexpression increased the number of cells with a migratory phenotype, in a potentially phosphatidylinositol 3 kinase (PI3K)–Ak strain transforming (AKT) mediated manner. Indeed, CD81 also co-localized with AKT, a CD81-interactor and actin remodeling agent, at the inner leaflet of the plasma membrane. Pharmacologic inhibition of PI3K, the canonical AKT activator, led both to a decrease in the acquisition of a migratory phenotype and to a redistribution of intracellular CD81 and F-actin into cytoplasmic agglomerates. These findings suggest that in neuronal-like cells CD81 bridges active AKT and actin, promoting the actin remodeling that leads to a motile cell morphology. Further studies on this CD81-mediated mechanism will improve our knowledge on important physiological and pathological processes such as cell migration and differentiation, and tumor metastasis.
Fabrication of Atom Probe Tomography Specimens from Nanoparticles Using a Fusible Bi–In–Sn Alloy as an Embedding Medium
Authors: Kim Se-Ho , Lee Ji Yeong , Ahn Jae-Pyoung , Choi Pyuck-Pa 
Published: February 2019

AbstractWe propose a new method for preparing atom probe tomography specimens from nanoparticles using a fusible bismuth–indium–tin alloy as an embedding medium. Iron nanoparticles synthesized by the sodium borohydride reduction method were chosen as a model system. The as-synthesized iron nanoparticles were embedded within the fusible alloy using focused ion beam milling and ion-milled to needle-shaped atom probe specimens under cryogenic conditions. An atom probe analysis revealed boron atoms in a detected iron nanoparticle, indicating that boron from the sodium borohydride reductant was incorporated into the nanoparticle during its synthesis.
Atom Probe Microscopy of Strengthening Effects in Alloy 718
Authors: Theska Felix , Ringer Simon Peter , Primig Sophie 
Published: February 2019

AbstractPolycrystalline Ni-based superalloys for aerospace and power generation applications are often precipitation hardened to achieve strengthening at elevated temperatures. Here, atom probe microscopy has become an essential tool to study the complex morphology of nanoscale precipitates. This study focuses on Alloy 718, which is hardened by semi-coherent, ordered γ′ (Ni3(Al, Ti)) and γ″ (Ni3(Nb)) particles. According to previous research, these particles often occur as duplets or triplets with a stacking sequence dependent on prior processing. This creates various interfaces with a strong impact on the mechanical properties, highlighting the importance of quantitative studies which are challenging with electron microscopy. We present atom probe data reconstruction and analysis approaches particularly suited for precipitation hardened superalloys. While voltage atom probe allows for an accurate reconstruction, the acquired data volume is often limited. Laser-assisted atom probe provides statistically significant data, but the loss of crystallographic information requires correlation with voltage-mode datasets. We further describe an advanced iso-surface method where initially arbitrarily chosen concentration thresholds of Al + Ti for γ′ and Nb for γ″ particles are optimized. Recognizing the importance of the precipitate stacking order, the different types of precipitate interfaces are quantified, and these methods may be applicable to other engineering alloys.
Micro-Raman Spectroscopy Reveals the Presence of Octacalcium Phosphate and Whitlockite in Association with Bacteria-Free Zones Within the Mineralized Dental Biofilm
Authors: Shah Furqan A. 
Published: February 2019

AbstractThrough a correlative analytical approach encompassing backscattered electron scanning electron microscopy (BSE-SEM), energy dispersive X-ray spectroscopy (EDX), and micro-Raman spectroscopy, the composition of the mineralized biofilm around a dental implant, retrieved due to peri-implantitis, was investigated. The mineralized biofilm contains two morphologically distinct regions: (i) bacteria-containing zones (Bact+), characterized by aggregations of unmineralized and mineralized bacteria, and intermicrobial mineralization, and (ii) bacteria-free zones (Bact−), comprised mainly of randomly oriented mineral platelets. Intramicrobial mineralization, within Bact+, appears as smooth, solid mineral deposits resembling the morphologies of dental plaque bacteria. Bact− is associated with micrometer-sized Mg-rich mineral nodules. The Ca/P ratio of Bact+ is higher than Bact−. The inorganic phase of Bact+ is carbonated apatite (CHAp), while that of Bact− is predominantly octacalcium phosphate (OCP) and whitlockite (WL) inclusions. Compared with native bone, the inorganic phase of Bact+ (i.e., CHAp) exhibits higher mineral crystallinity, lower carbonate content, and lower Ca/P, C/Ca, Mg/Ca, and Mg/P ratios. The various CaPs found within the mineralized dental biofilm (CHAp, OCP, and WL) are related to the local presence/absence of bacteria. In combination with BSE-SEM and EDX, micro-Raman spectroscopy is a valuable analytical tool for nondestructive investigation of mineralized dental biofilm composition and development.
The f-Ratio Quantification Method for X-ray Microanalysis Applied to Mg–Al–Zn Alloys
Authors: Teng Chaoyi , Demers Hendrix , Chu Xin , Gauvin Raynald 
Published: February 2019

AbstractThe f-ratio quantitative X-ray microanalysis method has been recently developed for binary systems based on a scanning electron microscope/energy dispersive spectroscopy (SEM/EDS) system. This method incorporates traditional EDS experiments and Monte Carlo simulations, and calibration factors are calculated with standard samples to evaluate the differences between them. In this work, the f-ratio method was extended to Mg–Al–Zn multi-element systems using a cold field emission SEM and a tungsten emission SEM. Results show that the stability of the beam current does not influence the f-ratio quantification accuracy. Thus, the f-ratio method is suitable for quantitative X-ray mapping with a long-time acquisition or even an unstable beam current. Comparing with other quantitative techniques including the routine standardless analysis and the standard-based k-ratio method, the f-ratio method is a simple and accurate quantification method.
Surface Diffusion of Fe and Cu on Fe (001) Under Electric Field Using First-Principles Calculations
Authors: Ohnuma Toshiharu 
Published: February 2019

AbstractFirst-principles calculations were performed to determine the Fe on Fe (001) evaporation field and to characterize the surface diffusion of Fe and Cu on Fe (001) and on a step structure under an applied electric field. The evaporation field of Fe on Fe (001) was calculated by the nudged elastic band (NEB) method, using the combination of the effective screening medium and constant electrode potential methods to obtain a condition of constant electric field. The calculated evaporation field of Fe on Fe (001) was 32.4 V/nm, which agrees well with the experimental value. In the surface diffusion of Fe and Cu on Fe (001) and on a step structure, the activation barrier energies were determined by the NEB method with constant applied electric field. It was found that Cu diffuse more easily on the Fe (001) and step structure than Fe under an applied electric field. The activation barrier energy of surface diffusion in the saddle point configuration is small when the distance between Cu and Fe on the surface is larger, and the activation barrier energy becomes smaller when passing through a path far away from the surface due to the effect of the electric field.
Application of Gray Level Co-Occurrence Matrix Analysis as a New Method for Enzyme Histochemistry Quantification
Authors: Dragić Milorad , Zarić Marina , Mitrović Nataša , Nedeljković Nadežda , Grković Ivana 
Published: February 2019

AbstractEnzyme histochemistry is a valuable histological method which provides a connection between morphology, activity, and spatial localization of investigated enzymes. Even though the method relies purely on arbitrary evaluations performed by the human eye, it is still wildly accepted and used in histo(patho)logy. Texture analysis emerged as an excellent tool for image quantification of subtle differences reflected in both spatial discrepancies and gray level values of pixels. The current study of texture analysis utilizes the gray-level co-occurrence matrix as a method for quantification of differences between ecto-5′-nucleotidase activities in healthy hippocampal tissue and tissue with marked neurodegeneration. We used the angular second moment, contrast (CON), correlation, inverse difference moment (INV), and entropy for texture analysis and receiver operating characteristic analysis with immunoblot and qualitative assessment of enzyme histochemistry as a validation. Our results strongly argue that co-occurrence matrix analysis could be used for the determination of fine differences in the enzyme activities with the possibility to ascribe those differences to regions or specific cell types. In addition, it emerged that INV and CON are especially useful parameters for this type of enzyme histochemistry analysis. We concluded that texture analysis is a reliable method for quantification of this descriptive technique, thus removing biases and adding it a quantitative dimension.
Trichome and biochemical basis of resistance against Tuta absoluta in tomato genotypes
Authors: Sridhar Vaddi , Sadashiva Avverahally Thammanna , Keshava Rao Vala , Swathi Padavala , Gadad Hanamant Shivalingappa 
Published: February 2019

AbstractSouth American tomato moth,Tuta absoluta, a serious pest of tomato (Solanum lycopersicum) in tropics and subtropics, is rapidly spreading world over. Twenty one wild/cultivated/advanced breeding lines of tomato were screened for resistance toT. absolutaunder greenhouse conditions (choice bioassay) and promising genotypes were evaluated further for their antibiosis activity through no choice bioassay underin-vitroconditions. From 21 genotypes screened, six wild accessions viz.,S. pennellii(LA 1940);S. chilense(LA 1963);S. arcanum(LA 2157);S. lycopersicum(LA1257) andS. corneliomulleri(LA 1292, LA1274) were relatively resistant toT. absolutabased on mean percent damage and were further studied underin-vitroconditions. These genotypes recorded relatively more larval mortality, prolonged larval and pupal duration with reduced adult emergence ofT. absoluta. Among these six genotypes,S. pennellii(LA-1940) showed resistance both under choice and no choice bioassays with higher number of type IV trichomes, highest total flavonoids and phenols. In general, glandular trichomes (GTs) (type I, IV, VII) showed negative correlation in different genotypes of tomato with reference to larval number/plant, percent damage and adult activity, whereas type V (non-GTs) showed negative correlation with number of larvae/plant.
Using Mutual Information to Determine Geoeffectiveness of Solar Wind Phase Fronts With Different Front Orientations
Authors: Cameron T. G. , Jackel B. , Oliveira D. M. 
Published: February 2019

AbstractThe geoeffectiveness of solar wind shocks depends on angle with respect to the Sun‐Earth line, with highly angled solar wind shocks being less geoeffective than nearly frontal solar wind shocks. However, it is unclear whether this holds for the orientation of structures in nonshocked solar wind. In this paper, we perform a mutual information analysis of 18 years of in situ solar wind and ground magnetometer data in order to investigate the effects of solar wind phase front orientation on solar wind geoeffectiveness (indicated by SuperMAG SME, the SuperMAG enhanced version of the AE index). Since geomagnetic response is strongly influenced by interplanetary magnetic field (IMF) Bz, and IMF Bz affects phase front orientation, we use conditional mutual information to account for the effect of Bz on geomagnetic activity. In contrast to what has been found for solar wind shocks, we find that during times of IMF Bz > 0, phase fronts aligned with the average Parker spiral direction (45° azimuth, 0° inclination) tend to be associated with higher geomagnetic activity (SME > 500 nT) than would be expected if IMF Bz and phase front orientation quantities were unrelated. During times of IMF Bz < 0, there is no connection between solar wind phase front orientation and geomagnetic activity (SME). We believe that Parker spiral‐aligned phase fronts being associated with higher geomagnetic activity during times of IMF Bz > 0 is due to constant phase front orientation allowing for more efficient energy transfer either through viscous interaction or high‐latitude reconnection.
Constraining the IMF at Pluto Using New Horizons SWAP Data and Hybrid Simulations
Authors: Barnes N. P. , Delamere P. A. , Strobel D. F. , Bagenal F. , McComas D. J. , Elliott H. A. , Valek P. , Weaver H. A. , Ennico K. , Young L. A. , Stern S. A. 
Published: February 2019

AbstractNew Horizons did not carry a magnetometer, so there is no direct way to know the strength of the Interplanetary Magnetic Field (IMF) at the time of the flyby. Using a hybrid model together with a detailed model of the Solar Wind Around Pluto (SWAP) instrument (McComas et al., 2007, https://doi.org/10.1007/s11214-007-9205-3) we have identified three observables that are sensitive to IMF strength: the width of Pluto's heavy ion tail, the energy of heavy ions, and the profile of thermal pressure along the New Horizons trajectory. By comparing simulation to data we infer that the IMF strength was most likely near or below ∼0.1 nT. We also show that the shell distribution of Interstellar Pickup Ions is important for reproducing these observations due to its effect on global pressure balance.
Acyl Peroxy Nitrates Link Oil and Natural Gas Emissions to High Ozone Abundances in the Colorado Front Range During Summer 2015
Authors: Lindaas Jakob , Farmer Delphine K. , Pollack Ilana B. , Abeleira Andrew , Flocke Frank , Fischer Emily V. 
Published: February 2019

AbstractWe present measurements of ozone (O3), acyl peroxy nitrates (APNs), and a suite of O3precursors made at the Boulder Atmospheric Observatory in Erie, Colorado, during summer 2015. We employ an empirical analysis of the APNs and a previously described positive matrix factorization of the volatile organic compounds (VOCs) to investigate the contribution of different VOC sources to high O3abundances at Boulder Atmospheric Observatory. Based on the ratio of peroxypropionyl nitrate (PPN) to peroxyacetyl nitrate (PAN), we find that anthropogenic VOC precursors dominate APN production when O3is most elevated. Propane and larger alkanes, primarily from oil and natural gas emissions in the Colorado Front Range, drive these elevated PPN to PAN ratios during high O3events. The percentage of OH reactivity associated with oil and gas emissions is also positively correlated with O3and PPN/PAN. Idealized box model simulations are used to probe the chemical mechanisms potentially responsible for these observations. We find that observed abundances of long‐lived oil and natural gas‐related VOCs are likely high enough such that the oxidation of these VOCs in a single photochemical day produces sufficient peroxy radicals to contribute to O3formation in the northern Colorado Front Range. Based on our empirical observations and box model simulations, we conclude that oil and natural gas emissions contribute to O3production on high O3days in this region during summer 2015.
Inconsistent Wind Speed Trends in Current Twentieth Century Reanalyses
Authors: Wohland Jan , Omrani Nour‐Eddine , Witthaut Dirk , Keenlyside Noel S. 
Published: February 2019

AbstractReanalysis data underpin much research in atmospheric and related sciences. While most reanalysis only cover the last couple of decades, National Oceanic and Atmospheric Administration (20CR) and European Centre for Medium‐Range Weather Forecasts (ERA20C and CERA20C) also developed reanalyses for the entire twentieth century that theoretically allow investigation of multidecadal variability. However, the approaches adopted to handle the massively evolving number of observations can cause spurious signals. Here we focus on wind speeds, as its assimilation is a key difference among these two products. We show that ERA20C and CERA20C feature significant trends in the North Atlantic and North Pacific wind speeds of up to 3 m/s per century. We show that there is a good relation between the trends in the reanalysis and assimilated wind speeds. In contrast, 20CR and the European Centre for Medium‐Range Weather Forecasts free model run ERA20CM do not show positive trends in the same regions. As a consequence, conclusions drawn from any single twentieth century reanalysis should be treated cautiously in particular in sectors with a strong wind dependency (e.g., wind energy).
Genome-wide by environment interaction studies of depressive symptoms and psychosocial stress in UK Biobank and Generation Scotland
Authors: Arnau-Soler Aleix , Macdonald-Dunlop Erin , Adams Mark J. , Clarke Toni-Kim , MacIntyre Donald J. , Milburn Keith , Navrady Lauren ,   Generation Scotland,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Hayward Caroline , McIntosh Andrew M. , Thomson Pippa A. 
Published: February 2019

AbstractStress is associated with poorer physical and mental health. To improve our understanding of this link, we performed genome-wide association studies (GWAS) of depressive symptoms and genome-wide by environment interaction studies (GWEIS) of depressive symptoms and stressful life events (SLE) in two UK population-based cohorts (Generation Scotland and UK Biobank). No SNP was individually significant in either GWAS, but gene-based tests identified six genes associated with depressive symptoms in UK Biobank (DCC, ACSS3, DRD2, STAG1, FOXP2 and KYNU; p < 2.77 × 10−6). Two SNPs with genome-wide significant GxE effects were identified by GWEIS in Generation Scotland: rs12789145 (53-kb downstream PIWIL4; p = 4.95 × 10−9; total SLE) and rs17070072 (intronic to ZCCHC2; p = 1.46 × 10−8; dependent SLE). A third locus upstream CYLC2 (rs12000047 and rs12005200, p < 2.00 × 10−8; dependent SLE) when the joint effect of the SNP main and GxE effects was considered. GWEIS gene-based tests identified: MTNR1B with GxE effect with dependent SLE in Generation Scotland; and PHF2 with the joint effect in UK Biobank (p < 2.77 × 10−6). Polygenic risk scores (PRSs) analyses incorporating GxE effects improved the prediction of depressive symptom scores, when using weights derived from either the UK Biobank GWAS of depressive symptoms (p = 0.01) or the PGC GWAS of major depressive disorder (p = 5.91 × 10−3). Using an independent sample, PRS derived using GWEIS GxE effects provided evidence of shared aetiologies between depressive symptoms and schizotypal personality, heart disease and COPD. Further such studies are required and may result in improved treatments for depression and other stress-related conditions.
Structural neuroimaging correlates of social deficits are similar in autism spectrum disorder and attention-deficit/hyperactivity disorder: analysis from the POND Network
Authors: Baribeau Danielle A. , Dupuis Annie , Paton Tara A. , Hammill Christopher , Scherer Stephen W. , Schachar Russell J. , Arnold Paul D. , Szatmari Peter , Nicolson Rob , Georgiades Stelios , Crosbie Jennifer , Brian Jessica , Iaboni Alana , Kushki Azadeh , Lerch Jason P. , Anagnostou Evdokia 
Published: February 2019

AbstractAutism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and obsessive-compulsive disorder (OCD) have been associated with difficulties recognizing and responding to social cues. Neuroimaging studies have begun to map the social brain; however, the specific neural substrates contributing to social deficits in neurodevelopmental disorders remain unclear. Three hundred and twelve children underwent structural magnetic resonance imaging of the brain (controls = 32, OCD = 44, ADHD = 77, ASD = 159; mean age = 11). Their social deficits were quantified on the Social Communication Questionnaire (SCQ) and the Reading the Mind in the Eyes Test (RMET). Multivariable regression models were used to examine the structural neuroimaging correlates of social deficits, with both a region of interest and a whole-brain vertex-wise approach. For the region of interest analysis, social brain regions were grouped into three networks: (1) lateral mentalization (e.g., temporal–parietal junction), (2) frontal cognitive (e.g., orbitofrontal cortex), and (3) subcortical affective (e.g., limbic system) regions. Overall, social communication deficits on the SCQ were associated with thinner cortices in the left lateral regions and the right insula, and decreased volume in the ventral striatum, across diagnostic groups (p = 0.006 to <0.0001). Smaller subcortical volumes were associated with more severe social deficits on the SCQ in ASD and ADHD, and less severe deficits in OCD. On the RMET, larger amygdala/hippocampal volumes were associated with fewer deficits across groups. Overall, patterns of associations were similar in ASD and ADHD, supporting a common underlying biology and the blurring of the diagnostic boundaries between these disorders.