bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explosive Volcanic Eruptions and Spinodal Decomposition: A Different Approach to Deciphering the Tiny Bubble Paradox
Authors: Sahagian Dork , Carley Tamara L. 
Published: May 2020

AbstractBubbles in magmas drive explosive volcanic eruptions. The spatial distribution of bubble nucleation sites in an ascending, decompressing, and supersaturating magma is one of the primary controls on ash morphologies and volcanic hazards. The mechanism of bubble formation is important because it ultimately determines the spatial distribution of bubbles in the fragmenting magma. The initial nucleation of bubbles in a homogeneous magma is problematical because excessive surface tension pressure in very small, nascent bubbles should drive exsolved volatiles back into the melt. This thermodynamic barrier to bubble viability confounds understanding of homogeneous bubble nucleation, yet very small bubbles form, grow, and ultimately drive explosive volcanic eruptions. We refer to this as “the tiny bubble paradox.” Classical nucleation theory typically explains bubble formation and growth, but we propose that a spectrum of bubble‐forming mechanisms may include both homogeneous nucleation and spinodal decomposition (the spontaneous unmixing of phases by uphill diffusion) as end‐member processes. As spinodal decomposition progresses, regularly sized and regularly spaced quasi‐spherical zones form with increasingly high concentration of dissolved water at the centers. Bubble formation occurs as the concentration of water in the interior of the water‐rich zones approaches 100% and the concentration of melt approaches zero. The presence of a broad, diffuse, concentration gradient of water rather than a narrow water‐melt interface means that there is no surface, per se, for surface tension to arise. This is the crux of the solution of the tiny bubble paradox.
Improvement of Atmospheric Objective Analysis Over Sloping Terrain and Its Impact on Shallow‐Cumulus Clouds in Large‐Eddy Simulations
Authors: Tang Shuaiqi , Xie Shaocheng , Zhang Minghua , Endo Satoshi 
Published: May 2020

AbstractSurface topography strongly impacts the regional atmospheric circulation dynamically and thermodynamically. Over the Great Plains in the United States, the gently tilted slope is an important factor that impacts clouds, convection, and regional circulations. This study enhances an atmospheric constrained variational analysis by using a terrain‐following sigma vertical coordinate and applies to the data collected at the Southern Great Plain (SGP) site of the Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) program. Sensitivity studies are performed to examine the impact of the terrain effects on the derived large‐scale atmospheric forcing fields and the simulated shallow‐cumulus clouds in large‐eddy simulation (LES) driven by the forcing. We found that the terrain impacts on the large‐scale forcing fields are mainly at lower levels and are strongly controlled by up/downslope winds. The response of the derived forcing to the slope of the terrain is monotonic, but the response of the simulated shallow‐cumulus clouds is more complex and depends on several factors. Overall, the terrain impact is small over SGP due to the small slope angle. However, the flat‐surface assumption may cause larger biases in the large‐scale forcing fields at locations with steeper terrain. The new sigma coordinate algorithm, with its consideration of surface slope, should be more suitable to derive large‐scale objective analysis over regions with steep terrain for application to force single‐column models, cloud resolving models, and LES models.
Multidimensional Channel Characteristics Analysis in High‐Speed Train Scenarios
Authors: Wu Zhigang , Ai Bo , Yang Jingya , Juhana Tutun , Wang Junhong , Li Yujian , Li Jing 
Published: May 2020

AbstractLTE for Railways (LTE‐R) is a next‐generation communication network dedicated to railway services, enabling high‐speed, reliable, and intelligent communications to ensure safety and efficiency for rail passengers. The wireless channel between the train and the ground is a key challenge in network design and optimization. The high‐speed train (HST) and its surrounding scenarios bring nonstationarity and unique radio propagation characteristics to the HST channel. A comprehensive and in‐depth analysis of channel characteristics is the basis of channel modeling. In this paper, based on the measurement‐validation ray tracing (RT) simulator, the quasi‐stationary intervals are presented first to reasonably quantify channel statistical parameters. Next, the time‐varying multidimensional spectra of the channels in three typical HST scenarios are shown, including the power delay profile (PDP), the arrival/departure angular spectrum, and the Doppler spectrum. Moreover, the corresponding channel characteristic parameters are extracted, such as the root‐mean‐square (RMS) delay spread, angular spread, and Doppler spread. Based on multidimensional channel characteristic analysis, combined with multipath geometric parameters provided by RT, we extract significant scatterers and mine key physical factors that affect radio propagation in HST scenarios. This work lays a solid foundation for accurate time‐varying HST channel modeling.
An Automatic In Situ Contact Angle Determination Based on Level Set Method
Authors: Yang Jianhui , Zhou Yingfang 
Published: May 2020

AbstractA novel level set‐based approach is presented to calculate in situ contact angle distribution, θ, from pore‐scale immiscible fluids and rock configuration directly imaged with micro‐computed tomography (micro‐CT) techniques. We first identify interfaces of the fluid‐fluid and fluid‐solid by their zero level set functions. This is accomplished by reinitializing the level set functions with a signed distance function. Then the three‐phase contact line is determined at the crossover of the two zero level set functions that represent the two interfaces. The normal vectors of both surfaces are calculated directly using the two level set functions, and the contact angle is found from the dot product of these vectors where they meet at the contact line. We first validated our newly proposed method for the semianalytically calculated fluid configurations in a 2‐D tube and then tested the algorithm on a synthetic spherical oil droplet residing on a tilted flat solid surface where the contact angle is analytically defined. It was then used to measure the in situ contact angle of droplets directly imaged by micro‐CT, and the results are compared with the manually and other available automatically measured results. Compared with other available automatic approaches, our approach is mathematically well defined, and it does not require any other complicated tuning procedures for surface smoothing. This proposed approach allow us to accurately characterize local in situ pore‐scale wettability, which is essential to model multiphase flow in porous media and eventually help us to design and assess optimal processes, such as hydrocarbon recovery and carbon dioxide storage.
H3K36 dimethylation by MMSET promotes classical non-homologous end-joining at unprotected telomeres
Authors: de Krijger Inge , van der Torre Jaco , Peuscher Marieke H. , Eder Mathias , Jacobs Jacqueline J. L. 
Published: May 2020

AbstractThe epigenetic environment plays an important role in DNA damage recognition and repair, both at DNA double-strand breaks and at deprotected telomeres. To increase understanding on how DNA damage responses (DDR) at deprotected telomeres are regulated by modification and remodeling of telomeric chromatin we screened 38 methyltransferases for their ability to promote telomere dysfunction-induced genomic instability. As top hit we identified MMSET, a histone methyltransferase (HMT) causally linked to multiple myeloma and Wolf-Hirschhorn syndrome. We show that MMSET promotes non-homologous end-joining (NHEJ) at deprotected telomeres through Ligase4-dependent classical NHEJ, and does not contribute to Ligase3-dependent alternative NHEJ. Moreover, we show that this is dependent on the catalytic activity of MMSET, enabled by its SET-domain. Indeed, in absence of MMSET H3K36-dimethylation (H3K36me2) decreases, both globally and at subtelomeric regions. Interestingly, the level of MMSET-dependent H3K36me2 directly correlates with NHEJ-efficiency. We show that MMSET depletion does not impact on recognition of deprotected telomeres by the DDR-machinery or on subsequent recruitment of DDR-factors acting upstream or at the level of DNA repair pathway choice. Our data are most consistent with an important role for H3K36me2 in more downstream steps of the DNA repair process. Moreover, we find additional H3K36me2-specific HMTs to contribute to NHEJ at deprotected telomeres, further emphasizing the importance of H3K36me2 in DNA repair.
Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase
Authors: Zhang Lilan , Xie Zhenzhen , Liu Ziwei , Zhou Shuyu , Ma Lixin , Liu Weidong , Huang Jian-Wen , Ko Tzu-Ping , Li Xiuqin , Hu Yuechan , Min Jian , Yu Xuejing , Guo Rey-Ting , Chen Chun-Chi 
Published: May 2020

AbstractCytochrome P450 monooxygenases are versatile heme-thiolate enzymes that catalyze a wide range of reactions. Self-sufficient cytochrome P450 enzymes contain the redox partners in a single polypeptide chain. Here, we present the crystal structure of full-length CYP116B46, a self-sufficient P450. The continuous polypeptide chain comprises three functional domains, which align well with the direction of electrons traveling from FMN to the heme through the [2Fe-2S] cluster. FMN and the [2Fe-2S] cluster are positioned closely, which facilitates efficient electron shuttling. The edge-to-edge straight-line distance between the [2Fe-2S] cluster and heme is approx. 25.3 Å. The role of several residues located between the [2Fe-2S] cluster and heme in the catalytic reaction is probed in mutagenesis experiments. These findings not only provide insights into the intramolecular electron transfer of self-sufficient P450s, but are also of interest for biotechnological applications of self-sufficient P450s.
Active colloidal molecules assembled via selective and directional bonds
Authors: Wang Zuochen , Wang Zhisheng , Li Jiahui , Tian Changhao , Wang Yufeng 
Published: May 2020

AbstractThe assembly of active and self-propelled particles is an emerging strategy to create dynamic materials otherwise impossible. However, control of the complex particle interactions remains challenging. Here, we show that various dynamic interactions of active patchy particles can be orchestrated by tuning the particle size, shape, composition, etc. This capability is manifested in establishing dynamic colloidal bonds that are highly selective and directional, which greatly expands the spectrum of colloidal structures and dynamics by assembly. For example, we demonstrate the formation of colloidal molecules with tunable bond angles and orientations. They exhibit controllable propulsion, steering, reconfiguration as well as other dynamic behaviors that collectively reflect the bond properties. The working principle is further extended to the co-assembly of synthetic particles with biological entities including living cells, giving rise to hybrid colloidal molecules of various types, for example, a colloidal carrousel structure. Our strategy should enable active systems to perform sophisticated tasks in future such as selective cell treatment.
Probe-target hybridization depends on spatial uniformity of initial concentration condition across large-format chips
Authors: Geldert Alisha , Huang Haiyan , Herr Amy E. 
Published: May 2020

AbstractDiverse assays spanning from immunohistochemistry (IHC), to microarrays (protein, DNA), to high-throughput screens rely on probe-target hybridization to detect analytes. These large-format ‘chips’ array numerous hybridization sites across centimeter-scale areas. However, the reactions are prone to intra-assay spatial variation in hybridization efficiency. The mechanism of spatial bias in hybridization efficiency is poorly understood, particularly in IHC and in-gel immunoassays, where immobilized targets are heterogeneously distributed throughout a tissue or hydrogel network. In these systems, antibody probe hybridization to a target protein antigen depends on the interplay of dilution, thermodynamic partitioning, diffusion, and reaction. Here, we investigate parameters governing antibody probe transport and reaction (i.e., immunoprobing) in a large-format hydrogel immunoassay. Using transport and bimolecular binding theory, we identify a regime in which immunoprobing efficiency (η) is sensitive to the local concentration of applied antibody probe solution, despite the antibody probe being in excess compared to antigen. Sandwiching antibody probe solution against the hydrogel surface yields spatially nonuniform dilution. Using photopatterned fluorescent protein targets and a single-cell immunoassay, we identify regimes in which nonuniformly distributed antibody probe solution causes intra-assay variation in background and η. Understanding the physicochemical factors affecting probe-target hybridization reduces technical variation in large-format chips, improving measurement precision.
Integration of Position and Predictive Motion Signals in Aging Vision
Authors: Jeon Hyun-Jun , Yun Yeojeong , Kwon Oh-Sang 
Published: May 2020

AbstractWe examined the effect of aging on the integration of position and motion signals, which is essential for tracking visual objects, using the motion-induced position shift (MIPS) phenomenon. We first measured the MIPS and bias in speed perception at three eccentricities. Both young and older adults showed the increasing MIPS and decreasing perceived speed as the eccentricity increased, which is consistent with previous literature. More importantly, we found that the mean MIPS was 2.87 times larger in older adults, and the response variability in position tasks showed a larger difference between age groups compared with the difference in speed tasks. We then measured the MIPS across stimulus durations. Temporal changes in the MIPS showed similar patterns in young and older adults in that the MIPS initially peaked at around 60 ms and approached an asymptote. We further analyzed the changes in response variability across stimulus durations to estimate sensory noise and propagation noise separately and found that only sensory noise was significantly larger in older adults. The overall results suggest that the increased MIPS in older adults is due to the increased dependency on predictive motion signals to compensate for the relatively imprecise position signals, which in turn implies that older adults would depend more on the motion signals to track objects.
Gearing Up the Human Ankle-Foot System to Reduce Energy Cost of Fast Walking
Authors: Ray Samuel F. , Takahashi Kota Z. 
Published: May 2020

AbstractDuring locomotion, the human ankle-foot system dynamically alters its gearing, or leverage of the ankle joint on the ground. Shifting ankle-foot gearing regulates speed of plantarflexor (i.e., calf muscle) contraction, which influences economy of force production. Here, we tested the hypothesis that manipulating ankle-foot gearing via stiff-insoled shoes will change the force-velocity operation of plantarflexor muscles and influence whole-body energy cost differently across walking speeds. We used in vivo ultrasound imaging to analyze fascicle contraction mechanics and whole-body energy expenditure across three walking speeds (1.25, 1.75, and 2.0 m/s) and three levels of foot stiffness. Stiff insoles increased leverage of the foot upon the ground (p < 0.001), and increased dorsiflexion range-of-motion (p < 0.001). Furthermore, stiff insoles resulted in a 15.9% increase in average force output (p < 0.001) and 19.3% slower fascicle contraction speed (p = 0.002) of the major plantarflexor (Soleus) muscle, indicating a shift in its force-velocity operating region. Metabolically, the stiffest insoles increased energy cost by 9.6% at a typical walking speed (1.25 m/s, p = 0.026), but reduced energy cost by 7.1% at a fast speed (2.0 m/s, p = 0.040). Stiff insoles appear to add an extra gear unavailable to the human foot, which can enhance muscular performance in a specific locomotion task.
Future heat waves over the Mediterranean from an Euro-CORDEX regional climate model ensemble
Authors: Molina M. O. , Sánchez E. , Gutiérrez C. 
Published: May 2020

AbstractHeat waves are among the most relevant extreme climatic events due to their effects on society, agriculture and environment. The aim of this work is to improve our understanding of heat waves over the Mediterranean basin during the 21st century from an ensemble of Regional Climate Models (RCMs). Focus has been placed on sensitivities to forcing global models, emissions scenarios and the RCM resolution, being the first work based on Euro-CORDEX simulations to fully analyze future heat waves in the Mediterranean. Heat wave features are studied with Warm Spell Duration Index (WSDI, duration) and Heat Wave Magnitude Index daily (HWMId, intensity). Results indicate a large increase by the end of the century in both intensity and length of heat waves from all emissions scenarios, global models, and regional models at any resolution. Exceptional heat waves observed early on the century could then become normal by the end of this period. Forcing global models and emissions scenarios play a major role. Clear added value on spatial distribution and heat wave indices are obtained from global to regional models dynamical downscaling, related to the important coastal or orographic aspects widely present over the Mediterranean.
A simple, rapid typing method for Streptococcus agalactiae based on ribosomal subunit proteins by MALDI-TOF MS
Authors: Rothen Julian , Sapugahawatte Dulmini Nanayakkara , Li Carmen , Lo Norman , Vogel Guido , Foucault Frédéric , Pflüger Valentin , Pothier Joёl F. , Blom Jochen , Daubenberger Claudia , Ip Margaret 
Published: May 2020

AbstractStreptococcus agalactiae (Group B Streptococcus, GBS), is a frequent human colonizer and a leading cause of neonatal meningitis as well as an emerging pathogen in non-pregnant adults. GBS possesses a broad animal host spectrum, and recent studies proved atypical GBS genotypes can cause human invasive diseases through animal sources as food-borne zoonotic infections. We applied a MALDI-TOF MS typing method, based on molecular weight variations of predefined 28 ribosomal subunit proteins (rsp) to classify GBS strains of varying serotypes into major phylogenetic lineages. A total of 249 GBS isolates of representative and varying capsular serotypes from patients and animal food sources (fish and pig) collected during 2016–2018 in Hong Kong were analysed. Over 84% (143/171) noninvasive carriage GBS strains from patients were readily typed into 5 globally dominant rsp-profiles. Among GBS strains from food animals, over 90% (57/63) of fish and 13% (2/15) of pig GBS matched with existing rsp-profiles, while the remainder were classified into two novel rsp-profiles and we failed to assign a fish strain into any cluster. MALDI-TOF MS allowed for high-throughput screening and simultaneous detection of novel, so far not well described GBS genotypes. The method shown here is rapid, simple, readily transferable and adapted for use in a diagnostic microbiology laboratory with potential for the surveillance of emerging GBS genotypes with zoonotic potential.
Effect of beta-based sterilization on P(VDF-TrFE-CFE) terpolymer for medical applications
Authors: Della Schiava Nellie , Pedroli Francesco , Thetpraphi Kritsadi , Flocchini Annalisa , Le Minh-Quyen , Lermusiaux Patrick , Capsal Jean-Fabien , Cottinet Pierre-Jean 
Published: May 2020

AbstractElectroactive polymers (EAP) are one of the latest generations of flexible actuators, enabling new approaches to propulsion and maneuverability. Among them, poly(vinylidene fluoride-trifluoroethylene-chlorofluoroethylene/chlorotrifluoroethylene), abbreviated terpolymer, with its multifunctional sensing and actuating abilities as well as its impressive electrostrictive behavior, especially when being doped with an plasticizer, has been demonstrated to be a good candidate for the development of low-cost flexible guidewire tip for endovascular surgery. To minimize the possibility of bacterial, fungal, or viral disease transmission, all medical instruments (especially components made from polymers) must be sterilized before introduction into the patient. Gamma/beta (γ/β) irradiation is considered to be one of the most efficient techniques for targeted reduction of microbials and viruses under low temperature, often without drastic alterations in device properties. However, radiation may cause some physical and chemical changes in polymers. A compromise is required to ensure sufficient radiation for microbial deactivation but minimal radiation to retain the material’s properties. The main idea of this study aims at assessing the electromechanical performances and thermal/dielectric properties of β-irradiated terpolymer-based sterilization treatment. Ionizing β-rays did not cause any significant risk to the neat/plasticized terpolymers, confirming the reliability of such electrostrictive materials for medical device development.
Computational analysis and verification of molecular genetic targets for glioblastoma
Authors: Xue Liang , Liu Haibing , Chen Yehuang , Wei Liangfeng , Hong Jingfang 
Published: May 2020

Abstract
Background: Glioblastoma (GBM) is the most common malignant brain tumor with a poor prognosis. The initial treatment for high-grade gliomas is surgical excision. However, even with concomitant use of radiation or chemotherapy, patients are still prone to recurrence. The specific pathogenesis of GBM is still controversial.
Methods: Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) between GBM and normal brain tissues were screened. P-value was obtained by Bayes test based on the limma package. Statistical significance was set as P-value &lt;0.05 and |Fold change (FC)| &gt; 0.2 (GSE90886); P-value &lt;0.05 and |FC| &gt; 1 (GSE116520, GSE103228). Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG), protein–protein interaction (PPI) network were performed. Hub genes were selected from miRNA target genes and DEGs. GBM and normal brain tissues were extracted to verify the expression.
Results: A total of 100 DEGs were overlapped in both datasets. Analysis of pathways and process enrichment tests indicated that ion transport, positive regulation of macromolecule metabolic process, cell cycle, axon guidance were enriched in the GBM. Sixteen hub genes were identified. Hub genes ADARB1 and neuropilin 1 (NRP1) were significantly associated with overall survival (OS) and disease-free survival (DFS) (P&lt;0.05). Eukaryotic translation termination factor 1 (ETF1) was associated with DFS (P&lt;0.05).
Conclusions: DEGs and DEMs were found between GBM tumor tissues and normal brain tissues. These biomarkers may be used as targets for early diagnosis and specific treatment.