bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Optical Properties of Ice Crystals for Multiclass Cloud Microphysics
Authors: Baek Sunghye , Bae Soo Ya 
Published: November 2018

AbstractNew optical properties of ice crystals were implemented in a general circulation model. Ebert and Curry's (1992, https://doi.org/10.1029/91JD02472) and Fu's (1996, https://doi.org/10.1175/1520‐0442(1996)009<2058:AAPOTS>2.0.CO;2) parameterizations are widely used in the general circulation model radiation scheme. However, the validity of the data is limited to an effective radius (size) of 130 or 140 μm. This limit exceeds the median of the effective radius of snow (~200 μm), which is computed from the multiclass cloud microphysics scheme. A comparable amount of snow exists in the upper atmosphere near the lower part of ice clouds. Although the cross section of snow (extinction probability) is smaller than cloud ice, its impact on radiation has not been properly considered so far. We constructed a new lookup table of optical properties based on recent data for an extended effective radius up to 500 μm. The old data (<130 μm) also need to be updated with a more recent and elaborate method. We processed extensive data provided by Yang et al. (2013, https://doi.org/10.1175/JAS‐D‐12‐039.1) and linked to the radiation module of the Korean Integrated Model (KIM). The new optical properties change the shortwave scattering features, thus increasing the heating rate. This tendency is checked in both one‐dimensional and global weather forecast simulations. With the new optical properties, KIM shows better performance by reducing bias with respect to the Integrated Forecasting Systems (IFS) analysis data.
Settling and Mobilization of Sand‐Fiber Proppants in a Deformable Fracture
Authors: Medina Ricardo , Detwiler Russell L. , Prioul Romain , Xu Wenyue , Elkhoury Jean E. 
Published: November 2018

AbstractWe investigated the response of a sand‐fiber proppant suspension (17.7% 40/70 mesh sand and 0.4% polymeric fibers) flowing and settling inside a transparent deformable 15 ×15‐cm fracture subjected to an increasing applied normal stress, σn. We quantified the solid distribution within the fracture and the evolution of the solid volume fraction, ϕ, as σn increased. The sand‐fiber suspension formed a highly heterogeneous proppant pack with sand‐fiber clumps surrounded by relatively solids‐free regions, which was significantly different from the uniform solid distribution observed in settling experiments without fibers. As σn increased from 0 to 88.5 kPa, the fracture aperture decreased by up to 85% and caused the sand‐fiber clumps to act like pillars that supported the applied stress and prevented full fracture closure. At the end of the settling experiments, we simulated flowback by injecting solids‐free carrier fluid while maintaining σn=88.5 kPa. Subsequent flow of solids‐free fluid caused the mobilization of some solids but left the supporting pillars intact. We used a numerical model to simulate flow through the porous proppant pack and open regions of the fracture and found a correlation between ϕ and the shear rate,
, at locations of mobilized solids, which suggested a mobilization threshold: ϕ<ϕmob and
. Additional simulations carried out in different heterogeneous proppant distributions showed that solid mobilization leads to the formation of highly conductive channels that significantly increase fracture permeability. Our results suggest that adding fibers to conventional sand proppants can lead to heterogeneous proppant distributions and increased fracture permeability.
Methylenetetrahydrofolate reductase and psychiatric diseases
Authors: Wan Lin , Li Yuhong , Zhang Zhengrong , Sun Zuoli , He Yi , Li Rena 
Published: November 2018

AbstractMethylenetetrahydrofolate reductase (MTHFR) is a key enzyme for the critical process of one-carbon metabolism involving folate and homocysteine metabolisms. It is known that some polymorphism of MTHFR would result in reduction of MTHFR enzyme activity as well as DNA methylation process, later shown to have significant impacts in various psychiatric diseases. However, it is unclear whether the polymorphism of MTHFR could be an independent or an add-on risk factor for specific psychiatric symptoms, such as anxiety, depression, positive, or negative symptoms of schizophrenia, or acts as risk factor for specific psychiatric disorders, such as schizophrenia, major depression, autisms, and bipolar disorders. It is also understudied on whether folate supplements could be an effective treatment for psychiatric patients with defect MTHFR activity. In this review, we not only gathered the most recent discoveries on MTHFR polymorphism and related DNA methylation in various psychiatric disorders, but also highlighted the potential relationships between MTHFR activity and implication of folate-related function in specific mental diseases.
A Chiron approach towards the stereoselective synthesis of polyfluorinated carbohydrates
Authors: Denavit Vincent , Lainé Danny , St-Gelais Jacob , Johnson Paul A. , Giguère Denis 
Published: November 2018

AbstractThe replacement of hydroxyl groups by fluorine atoms on hexopyranose scaffolds may allow access to the discovery of new chemical entities possessing unique physical, chemical and ultimately even biological properties. The prospect of significant effects generated by such multiple and controlled substitutions encouraged us to develop diverse synthetic routes towards the stereoselective synthesis of polyfluorinated hexopyranoses, six of which are unprecedented. Hence, we report the synthesis of heavily fluorinated galactose, glucose, mannose, talose, allose, fucose, and galacturonic acid methyl ester using a Chiron approach from inexpensive levoglucosan. Structural analysis of single-crystal X-ray diffractions and NMR studies confirm the conservation of favored 4C1 conformation for fluorinated carbohydrate analogs, while a slightly distorted conformation due to repulsive 1,3-diaxial F···F interaction is observed for the trifluorinated talose derivative. Finally, the relative stereochemistry of multi-vicinal fluorine atoms has a strong effect on the lipophilicities (logP).
Unusually complex phase of dense nitrogen at extreme conditions
Authors: Turnbull Robin , Hanfland Michael , Binns Jack , Martinez-Canales Miguel , Frost Mungo , Marqués Miriam , Howie Ross T. , Gregoryanz Eugene 
Published: November 2018

AbstractNitrogen exhibits an exceptional polymorphism under extreme conditions, making it unique amongst the elemental diatomics and a valuable testing system for experiment-theory comparison. Despite attracting considerable attention, the structures of many high-pressure nitrogen phases still require unambiguous determination. Here, we report the structure of the elusive high-pressure high-temperature polymorph ι–N2 at 56 GPa and ambient temperature, determined by single crystal X-ray diffraction, and investigate its properties using ab initio simulations. We find that ι–N2 is characterised by an extraordinarily large unit cell containing 48 N2 molecules. Geometry optimisation favours the experimentally determined structure and density functional theory calculations find ι–N2 to have the lowest enthalpy of the molecular nitrogen polymorphs that exist between 30 and 60 GPa. The results demonstrate that very complex structures, similar to those previously only observed in metallic elements, can become energetically favourable in molecular systems at extreme pressures and temperatures.
Neodymium isotope evidence for glacial-interglacial variability of deepwater transit time in the Pacific Ocean
Authors: Hu Rong , Piotrowski Alexander M. 
Published: November 2018

AbstractThere is evidence for greater carbon storage in the glacial deep Pacific, but it is uncertain whether it was caused by changes in ventilation, circulation, and biological productivity. The spatial εNd evolution in the deep Pacific provides information on the deepwater transit time. Seven new foraminiferal εNd records are presented to systematically constrain glacial to interglacial changes in deep Pacific overturning and two different εNd evolution regimes occur spatially in the Pacific with reduced meridional εNd gradients in glacials, suggesting a faster deep Pacific overturning circulation. This implies that greater glacial carbon storage due to sluggish circulation, that is believed to have occurred in the deep Atlantic, did not operate in a similar manner in the Pacific Ocean. Other mechanisms such as increased biological pump efficiency and poor high latitude air-sea exchange could be responsible for increased carbon storage in the glacial Pacific.
Perineuronal nets decrease membrane capacitance of peritumoral fast spiking interneurons in a model of epilepsy
Authors: Tewari Bhanu P. , Chaunsali Lata , Campbell Susan L. , Patel Dipan C. , Goode Adam E. , Sontheimer Harald 
Published: November 2018

AbstractBrain tumor patients commonly present with epileptic seizures. We show that tumor-associated seizures are the consequence of impaired GABAergic inhibition due to an overall loss of peritumoral fast spiking interneurons (FSNs) concomitant with a significantly reduced firing rate of those that remain. The reduced firing is due to the degradation of perineuronal nets (PNNs) that surround FSNs. We show that PNNs decrease specific membrane capacitance of FSNs permitting them to fire action potentials at supra-physiological frequencies. Tumor-released proteolytic enzymes degrade PNNs, resulting in increased membrane capacitance, reduced firing, and hence decreased GABA release. These studies uncovered a hitherto unknown role of PNNs as an electrostatic insulator that reduces specific membrane capacitance, functionally akin to myelin sheaths around axons, thereby permitting FSNs to exceed physiological firing rates. Disruption of PNNs may similarly account for excitation-inhibition imbalances in other forms of epilepsy and PNN protection through proteolytic inhibition may provide therapeutic benefits.
Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution
Authors: Roscito Juliana G. , Sameith Katrin , Parra Genis , Langer Bjoern E. , Petzold Andreas , Moebius Claudia , Bickle Marc , Rodrigues Miguel Trefaut , Hiller Michael 
Published: November 2018

AbstractDetecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits.
Plant defences mediate interactions between herbivory and the direct foliar uptake of atmospheric reactive nitrogen
Authors: Campbell Stuart A. , Vallano Dena M. 
Published: November 2018

AbstractReactive nitrogen from human sources (e.g., nitrogen dioxide, NO2) is taken up by plant roots following deposition to soils, but can also be assimilated by leaves directly from the atmosphere. Leaf uptake should alter plant metabolism and overall nitrogen balance and indirectly influence plant consumers; however, these consequences remain poorly understood. Here we show that direct foliar assimilation of NO2increases levels of nitrogen-based defensive metabolites in leaves and reduces herbivore consumption and growth. These results suggest that atmospheric reactive nitrogen could have cascading negative effects on communities of herbivorous insects. We further show that herbivory induces a decrease in foliar uptake, indicating that consumers could limit the ability of vegetation to act as a sink for nitrogen pollutants (e.g., smog from mobile emissions). Our study suggests that the interactions of foliar uptake, plant defence and herbivory could have significant implications for understanding the environmental consequences of reactive nitrogen.
N2H4 as traceless mediator for homo- and cross- aryl coupling
Authors: Lv Leiyang , Qiu Zihang , Li Jianbin , Liu Mingxin , Li Chao-Jun 
Published: November 2018

AbstractTransition-metal catalyzed couplings of aryl halides or arenes with aryl organometallics, as well as direct reductive coupling of two aryl halides, are the predominant methods to synthesize biaryls. However, stoichiometric amounts of metals are inevitably utilized in these reactions, either in the pre-generation of organometallic reagents or acting as reductant in situ, thus producing quantitative metal waste. Herein, we demonstrate that this longstanding challenge can be overcome with N2H4 as a metal surrogate. The fundamental innovation of this strategy is that N2 and H2 are generated as side products, which readily escape from the system after the reaction. The success of both homo- and cross-coupling of various aryl electrophiles bearing a wide range of functional groups manifests the powerfulness and versatility of this strategy. Furthermore, both homo- and cross-couplings of a series of alkaloids, amino acids and steroids exemplify application of this protocol in the functionalization of biologically active molecules.
Transcriptome-wide identification of transient RNA G-quadruplexes in human cells
Authors: Yang Sunny Y. , Lejault Pauline , Chevrier Sandy , Boidot Romain , Robertson A. Gordon , Wong Judy M. Y. , Monchaud David 
Published: November 2018

AbstractGuanine-rich RNA sequences can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), whose biological roles are poorly understood, and in vivo existence is debated. To profile biologically relevant G4-RNA in the human transcriptome, we report here on G4RP-seq, which combines G4-RNA-specific precipitation (G4RP) with sequencing. This protocol comprises a chemical crosslinking step, followed by affinity capture with the G4-specific small-molecule ligand/probe BioTASQ, and target identification by sequencing, allowing for capturing global snapshots of transiently folded G4-RNAs. We detect widespread G4-RNA targets within the transcriptome, indicative of transient G4 formation in living human cells. Using G4RP-seq, we also demonstrate that G4-stabilizing ligands (BRACO-19 and RHPS4) can change the G4 transcriptomic landscape, most notably in long non-coding RNAs. G4RP-seq thus provides a method for studying the G4-RNA landscape, as well as ways of considering the mechanisms underlying G4-RNA formation, and the activity of G4-stabilizing ligands.
An autonomous quantum machine to measure the thermodynamic arrow of time
Authors: Monsel Juliette , Elouard Cyril , Auffèves Alexia 
Published: November 2018

AbstractAccording to the second law of thermodynamics, the evolution of physical systems has a preferred direction, that is characterized by some positive entropy production. Here we propose a direct way to measure the stochastic entropy produced while driving a quantum open system out of thermal equilibrium. The driving work is provided by a quantum battery, the system and the battery forming an autonomous machine. We show that the battery’s energy fluctuations equal work fluctuations and check Jarzynski’s equality. As these energy fluctuations are measurable, the battery behaves as an embedded quantum work meter and the machine verifies a generalized fluctuation theorem involving the information encoded in the battery. Our proposal can be implemented with state-of-the-art opto-mechanical systems. It paves the way toward the experimental demonstration of fluctuation theorems in quantum open systems.
The effect of non-thermal atmospheric plasma on the production and activity of recombinant phytase enzyme
Authors: Farasat Mahsa , Arjmand Sareh , Ranaei Siadat Seyed Omid , Sefidbakht Yahya , Ghomi Hamid 
Published: November 2018

AbstractAtmospheric pressure cold plasma (ACP) is introduced as a useful tool in a variety of biological applications. Proteins are the most abundant macromolecules in living systems with a central role in all biological processes. These organic molecules are modified by ACP exposure that is responsible for many of ACP’s biological effects. This study evaluated the effect of ACP on the production of recombinant phytase in yeast Pichia pastoris (P. pastoris) as well as the structure and function of the phytase enzyme. The results indicated that yeast cells treated with ACP, directly or indirectly, produced higher amounts of recombinant phytase, which was associated with the time of ACP treatment. The exposure of commercial phytase solution with ACP caused a significant increase in the enzyme activity (125%) after 4 hours. Evaluation of the phytase solution by far- and near-UV circular dichroism (CD) and fluorescence analysis indicated that this protein maintained its secondary structure when exposed to ACP while the tertiary structure was slightly unfolded. The effects of heat and H2O2 on the phytase structure and function were compared with the effect of ACP treatment. The modification of Cys, Tyr and Trp amino acids upon reactive oxygen/nitrogen spices was simulated using a molecular dynamics approach. RMSF and RMSD analysis suggested that this structural alteration occurs owing to changes made by reactive species in accessible amino acids.
p.(Asp47Asn) and p.(Thr62Met): non deleterious LDL receptor missense variants functionally characterized in vitro
Authors: Benito-Vicente A. , Siddiqi H. , Uribe K. B. , Jebari S. , Galicia-Garcia U. , Larrea-Sebal A. , Stef M. , Ostolaza H. , Palacios L. , Martin C. 
Published: November 2018

AbstractFamilial Hypercholesterolemia (FH) is a common genetic disorder caused most often by mutations in the Low Density Lipoprotein Receptor gene (LDLr) leading to high blood cholesterol levels, and ultimately to development of premature coronary heart disease. Genetic analysis and subsequent cascade screening in relatives allow diagnosis of FH at early stage, especially relevant to diagnose children. So far, more than 2300 LDLr variants have been described but only a minority of them have been functionally analysed to evaluate their pathogenicity in FH. Thus, identifying pathogenic mutations in LDLr is a long-standing challenge in the field. In this study, we investigated in vitro the activity p.(Asp47Asn) and p.(Thr62Met) LDLr variants, both in the LR1 region. We used CHO-ldlA7 transfected cells with plasmids carrying p.(Asp47Asn) or p.(Thr62Met) LDLr variants to analyse LDLr expression by FACS and immunoblotting, LDL binding and uptake was determined by FACS and analysis of mutation effects was assessed in silico. The in vitro activity assessment of p.(Asp47Asn) and p.(Thr62Met) LDLr variants shows a fully functional LDL binding and uptake activities. Therefore indicating that the three of them are non-pathogenic LDLr variants. These findings also emphasize the importance of in vitro functional LDLr activity studies to optimize the genetic diagnosis of FH avoiding the report of non-pathogenic variants and possible misdiagnose in relatives if cascade screening is carried out.
Effect of selected biocides on microbiologically influenced corrosion caused by Desulfovibrio ferrophilus IS5
Authors: Sharma Mohita , Liu Hongwei , Chen Shiqiang , Cheng Frank , Voordouw Gerrit , Gieg Lisa 
Published: November 2018

AbstractThe marine bacterial strain Desulfovibrio ferrophilus IS5, known for its lithotrophic growth ability to use metallic iron as a sole electron donor and for causing corrosion of steel, was used in the current study. Four commonly used biocides in the oil and gas industry, namely tetrakis(hydroxymethyl) phosphonium sulfate (THPS), glutaraldehyde (GLUT), benzalkonium chloride (BAC), and GLUT/BAC were selected to study their efficacy in controlling carbon steel corrosion in the presence of this strain. Incubations containing strain IS5 and low carbon steel coupons were prepared in the presence and absence of the four biocides, and these were monitored using both electrochemical methods (electrochemical impedance spectroscopy, linear polarization resistance and potentiodynamic polarization) and surface analyses (scanning electron microscopy, confocal measurements, optical microscopy, and profilometry) to assess the biofilm/metal interactions. When THPS, BAC, and GLUT/BAC treatments were applied, minimal corrosion was measured by all methods. In contrast, severe pitting was observed in the presence of 50 ppm GLUT, similar to what was observed when D. ferrophilus IS5 was incubated in the absence of biocide, suggesting that GLUT alone may not be effective in controlling MIC in marine environments. This study also showed that the use of non-destructive electrochemical methods is effective for screening for real time biocide selection and monitoring of the impact of chemicals post-dosage in oil and gas operations.
High-throughput neutralization assay for multiple flaviviruses based on single-round infectious particles using dengue virus type 1 reporter replicon
Authors: Matsuda Mami , Yamanaka Atsushi , Yato Keigo , Yoshii Kentaro , Watashi Koichi , Aizaki Hideki , Konishi Eiji , Takasaki Tomohiko , Kato Takanobu , Muramatsu Masamichi , Wakita Takaji , Suzuki Ryosuke 
Published: November 2018

AbstractDiseases caused by the genus Flavivirus, including dengue virus (DENV) and Zika virus (ZIKV), have a serious impact on public health worldwide. Due to serological cross-reactivity among flaviviruses, current enzyme-linked immunosorbent assay (ELISA) for IgM/G cannot reliably distinguish between infection by different flaviviruses. In this study, we developed a reporter-based neutralization assay using single-round infectious particles (SRIPs) derived from representative flaviviruses. SRIPs were generated by transfection of human embryonic kidney 293 T cells with a plasmid encoding premembrane and envelope (prME) proteins from DENV1–4, ZIKV, Japanese encephalitis virus, West Nile virus, yellow fever virus, Usutu virus, and tick-borne encephalitis virus, along with a plasmid carrying DENV1 replicon containing the luciferase gene and plasmid for expression of DENV1 capsid. Luciferase activity of SRIPs-infected cells was well correlated with number of infected cells, and each reporter SRIP was specifically neutralized by sera from mice immunized with each flavivirus antigen. Our high-throughput reporter SRIP-based neutralization assay for multiple flaviviruses is a faster, safer, and less laborious diagnostic method than the conventional plaque reduction neutralization test to screen the cause of primary flavivirus infection. The assay may also contribute to the evaluation of vaccine efficacy and assist in routine surveillance and outbreak response to flaviviruses.