bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the Uncertainty of a Coupled Plume and Tephra Dispersal Model: PLUME‐MOM/HYSPLIT Simulations Applied to Andean Volcanoes
Authors: Tadini A. , Roche O. , Samaniego P. , Guillin A. , Azzaoui N. , Gouhier M. , de' Michieli Vitturi M. , Pardini F. , Eychenne J. , Bernard B. , Hidalgo S. , Le Pennec J. L. 
Published: January 2020

AbstractNumerical modeling of tephra dispersal and deposition is essential for evaluation of volcanic hazards. Many models consider reasonable physical approximations in order to reduce computational times, but this may introduce a certain degree of uncertainty in the simulation outputs. The important step of uncertainty quantification is dealt in this paper with respect to a coupled version of a plume model (PLUME‐MoM) and a tephra dispersal model (HYSPLIT). The performances of this model are evaluated through simulations of four past eruptions of different magnitudes and styles from three Andean volcanoes, and the uncertainty is quantified by evaluating the differences between modeled and observed data of plume height (at different time steps above the vent) as well as mass loading and grain size at given stratigraphic sections. Different meteorological data sets were also tested and had a sensible influence on the model outputs. Other results highlight that the model tends to underestimate plume heights while overestimating mass loading values, especially for higher‐magnitude eruptions. Moreover, the advective part of HYSPLIT seems to work more efficiently than the diffusive part. Finally, though the coupled PLUME‐MoM/HYSPLIT model generally is less efficient in reproducing deposit grain sizes, we propose that it may be used for hazard map production for higher‐magnitude eruptions (sub‐Plinian or Plinian) for what concern mass loading.
Mapping the Four‐Dimensional Viscosity Field of an Experimental Lava Flow
Authors: Farrell James A. 
Published: January 2020

AbstractViscosity is a critical rheological property that determines the behavior, evolution, and final morphology of lava flows. Determining the viscosity of an active lava flow, however, is nontrivial. The rheological structure of lava is complex, and during active flow conditions, viscosity can change by orders of magnitude through space and time. This makes viscosity one of the most elusive properties of flowing lava. After almost a century of research on lava viscosity, it is still common practice to reduce the viscosity of a flow to a single value, generalizing an immense field of deviations and complexities. Considering lava viscosity as a one‐dimensional variable may be sufficient for characterizing some aspects of flows, but it does not allow for solving higher‐order rheological problems, such as depth structure, spatial variability, or rates of change. This study presents, for the first time, the four‐dimensional viscosity field of an actively flowing experimental lava. Results from this experiment include time‐series thickness, surface velocity, and temperature maps that are used to solve for the 4‐D viscosity of the lava flow with a spatial resolution of 2 cm. Additionally, the approach used in this study allows for an analysis of vertical rheological structure, specifically, crust and core viscosity layers. Although this study was performed in an experimental setting with crystal‐ and bubble‐free lava, the basic data collection techniques applied are common in field volcanology and thus could be applicable in certain natural settings.
Millimeter‐Wave Radiometric Information Content Analysis for Venus Atmospheric Constituents
Authors: Mathew N. , Sahoo S. , Pillai R. Ramachandran , Raju C. Suresh 
Published: January 2020

AbstractVarious gaseous constituents present in Venus atmosphere have been detected and measured using in situ and remote sensing instruments. However, the measurements of mesospheric constituents above the cloud level are still scarce and inadequate. This is because constituents above the cloud level have a low abundance and a high level of variability. However, millimeter and submillimeter (mm and sub‐mm) frequencies can be used for Venus mesosphere measurements during prolonged Venusian day and night because several minor species in the upper atmosphere have emission/absorption bands in these frequencies owing to the rotational transitions. This study presents brightness temperatures and the corresponding sensitivity at the mm and sub‐mm wave frequencies for a limb sounding radiometer. This will be useful in potential payload design, that is, instrument design, frequency, bandwidth selection, and satellite altitude as well as pointing accuracy determination for measurement above Venus clouds. For this study, a simulation based experiment has been performed and presented to determine the mm and sub‐mm wave frequencies, optimum for estimation of concentration of water vapor, CO, CO2, SO2, HDO, and HCl present in the mesosphere. The simulations have been performed using a radiative transfer model called Atmospheric Radiative Transfer Simulator. The mm and sub‐mm wave measurement frequencies have been determined for both day and night time of Venus. It has been determined that 183, 380, 448, and 556 GHz frequencies are most suitable for water vapor measurements, 115, 230, and 345 GHz are optimum for CO measurements, and 600, 621, and 690 GHz frequency measurements are sensitive for HCl detection.
Acousto-optic modulation of photonic bound state in the continuum
Authors: Yu Zejie , Sun Xiankai 
Published: January 2020

AbstractPhotonic bound states in the continuum (BICs) have recently been studied in various systems and have found wide applications in sensors, lasers, and filters. Applying BICs in photonic integrated circuits enables low-loss light guidance and routing in low-refractive-index waveguides on high-refractive-index substrates, which opens a new avenue for integrated photonics with functional single-crystal materials. Here, we demonstrate high-quality integrated lithium niobate microcavities inside which the photonic BIC modes circulate and further modulate these BIC modes acousto-optically by using piezoelectrically actuated surface acoustic waves at microwave frequencies. With a high acousto-optic modulation frequency, the acousto-optic coupling is well situated in the resolved-sideband regime. This leads to coherent coupling between microwave and optical photons, which is exhibited by the observed electro-acousto-optically induced transparency and absorption. Therefore, our devices serve as a paradigm for manipulating and controlling photonic BICs on a chip, which will enable many other applications of photonic BICs in the areas of microwave photonics and quantum information processing.
Repurposing a psychoactive drug for children with cancer: p27Kip1-dependent inhibition of metastatic neuroblastomas by Prozac
Authors: Bibbo’ Sandra , Lamolinara Alessia , Capone Emily , Purgato Stefania , Tsakaneli Alexia , Panella Valeria , Sallese Michele , Rossi Cosmo , Ciufici Paolo , Nieddu Valentina , De Laurenzi Vincenzo , Iezzi Manuela , Perini Giovanni , Sala Gianluca , Sala Arturo 
Published: January 2020

AbstractThe MYC family of transcription factors is a major driver of human cancer and potential therapeutic target. However, no clinically viable drugs have been yet developed that are able to directly tackle MYC oncoproteins. In our laboratory, we are exploring alternative approaches aiming to disturb signalling downstream of MYC. MYCN is frequently activated in neuroblastoma, a paediatric solid malignancy that, in its metastatic form, has a very poor prognosis. An important pathway regulated by MYC is the CKS1/SKP2/p27kip1 axis. In this study, we have repurposed the anti-psychotic drug Prozac to disrupt CKS1/SKP2/p27Kip1 signalling and assess its potential as an anti-neuroblastoma agent in vitro and in vivo. Using DNA editing technology, we show that stabilisation of p27Kip1 operated by Prozac in MYC-activated cells is essential for the anti-neuroblastoma activity of the drug. Furthermore, dosing mice with a concentration of Prozac equivalent to that used in long-term clinical trials in children with psychiatric disorders caused a significant reduction of metastatic disease in two models of high-risk neuroblastoma. The favourable toxicity profile of Prozac suggests that long-term treatments might be implemented in children with MYC/CKS1high neuroblastomas.
DDIAS promotes STAT3 activation by preventing STAT3 recruitment to PTPRM in lung cancer cells
Authors: Im Joo-Young , Kim Bo-Kyung , Lee Kang-Woo , Chun So-Young , Kang Mi-Jung , Won Misun 
Published: January 2020

AbstractDNA damage-induced apoptosis suppressor (DDIAS) regulates cancer cell survival. Here we investigated the involvement of DDIAS in IL-6–mediated signaling to understand the mechanism underlying the role of DDIAS in lung cancer malignancy. We showed that DDIAS promotes tyrosine phosphorylation of signal transducer and activator of transcription 3 (STAT3), which is constitutively activated in malignant cancers. Interestingly, siRNA protein tyrosine phosphatase (PTP) library screening revealed protein tyrosine phosphatase receptor mu (PTPRM) as a novel STAT3 PTP. PTPRM knockdown rescued the DDIAS-knockdown-mediated decrease in STAT3 Y705 phosphorylation in the presence of IL-6. However, PTPRM overexpression decreased STAT3 Y705 phosphorylation. Moreover, endogenous PTPRM interacted with endogenous STAT3 for dephosphorylation at Y705 following IL-6 treatment. As expected, PTPRM bound to wild-type STAT3 but not the STAT3 Y705F mutant. PTPRM dephosphorylated STAT3 in the absence of DDIAS, suggesting that DDIAS hampers PTPRM/STAT3 interaction. In fact, DDIAS bound to the STAT3 transactivation domain (TAD), which competes with PTPRM to recruit STAT3 for dephosphorylation. Thus we show that DDIAS prevents PTPRM/STAT3 binding and blocks STAT3 Y705 dephosphorylation, thereby sustaining STAT3 activation in lung cancer. DDIAS expression strongly correlates with STAT3 phosphorylation in human lung cancer cell lines and tissues. Thus DDIAS may be considered as a potential biomarker and therapeutic target in malignant lung cancer cells with aberrant STAT3 activation.
The antibody response induced FMDV vaccines in sheep correlates with early transcriptomic responses in blood
Authors: Jouneau Luc , Lefebvre David J. , Costa Fleur , Romey Aurore , Blaise-Boisseau Sandra , Relmy Anthony , Jaszczyszyn Yan , Dard-Dascot Cloelia , Déjean Sébastien , Versillé Nicolas , Guitton Edouard , Hudelet Pascal , Curet Marianne , De Clercq Kris , Bakkali-Kassimi Labib , Zientara Stéphan , Klonjkowski Bernard , Schwartz-Cornil Isabelle 
Published: January 2020

AbstractFoot and mouth disease (FMD) is a highly contagious viral disease with high economic impact, representing a major threat for cloven-hooved mammals worldwide. Vaccines based on adjuvanted inactivated virus (iFMDV) induce effective protective immunity implicating antibody (Ab) responses. To reduce the biosafety constraints of the manufacturing process, a non-replicative human adenovirus type 5 vector encoding FMDV antigens (Ad5-FMDV) has been developed. Here we compared the immunogenicity of iFMDV and Ad5-FMDV with and without the ISA206VG emulsion-type adjuvant in sheep. Contrasted Ab responses were obtained: iFMDV induced the highest Ab levels, Ad5-FMDV the lowest ones, and ISA206VG increased the Ad5-FMDV-induced Ab responses to protective levels. Each vaccine generated heterogeneous Ab responses, with high and low responders, the latter being considered as obstacles to vaccine effectiveness. A transcriptomic study on total blood responses at 24 h post-vaccination revealed several blood gene module activities correlating with long-term Ab responses. Downmodulation of T cell modules’ activities correlated with high responses to iFMDV and to Ad5-FMDV+ISA206VG vaccines as also found in other systems vaccinology studies in humans and sheep. The impact of cell cycle activity depended on the vaccine types, as it positively correlated with higher responses to iFMDV but negatively to non-adjuvanted Ad5-FMDV. Finally an elevated B cell activity at 24 h correlated with high Ab responses to the Ad5-FMDV+ISA206VG vaccine. This study provides insights into the early mechanisms driving the Ab response induced by different vaccine regimens including Ad5 vectors and points to T cell modules as early biomarker candidates of different vaccine-type efficacy across species.
Acousto optic imaging beyond the acoustic diffraction limit using speckle decorrelation
Authors: Doktofsky Daniel , Rosenfeld Moriya , Katz Ori 
Published: January 2020

AbstractAcousto-optic imaging (AOI) enables optical-contrast imaging deep inside scattering samples via localized ultrasound modulation of scattered light. However, the resolution in AOI is inherently limited by the ultrasound focus size, prohibiting microscopic investigations. In recent years advances in the field of digital wavefront-shaping allowed the development of novel approaches for overcoming AOI’s acoustic resolution limit. However, these approaches require thousands of wavefront measurements within the sample speckle decorrelation time, limiting their application to static samples. Here, we show that it is possible to surpass the acoustic resolution-limit with a conventional AOI system by exploiting the natural dynamics of speckle decorrelations rather than trying to overcome them. We achieve this by adapting the principles of super-resolution optical fluctuations imaging (SOFI) to AOI. We show that naturally fluctuating optical speckle grains can serve in AOI as the analogues of blinking fluorophores in SOFI, enabling super-resolution by statistical analysis of fluctuating acousto-optic signals.
Microphthalmia, Linear Skin Defects, Callosal Agenesis, and Cleft Palate in a Patient with Deletion at Xp22.3p22.2
Authors: Vendramini-Pittoli Siulan , Candido-Souza Rosana Maria , Quiezi Rodrigo Gonçalves , Zechi-Ceide Roseli Maria , Kokitsu-Nakata Nancy Mizue , Jehee Fernanda Sarquis , Ribeiro-Bicudo Lucilene Arilho , FitzPatrick David R. , Guion-Almeida Maria Leine , Richieri-Costa Antonio 
Published: January 2020

AbstractThe authors describe the clinical findings observed in a Brazilian girl that are suggestive of microphthalmia and linear skin defects (MLS) also known as MIDAS syndrome (OMIM #309801). She also presented with short stature, agenesis of corpus callosum, cleft palate, enamel defects, and genitourinary anomalies, which are rarely reported within the clinical spectrum of MLS. The 11,5 Mb deletion in Xp22.3p22.2 observed in the patient includes the entire HCCS gene (responsible for the MLS phenotype) and also encompasses several other genes involved with behavioral phenotypes, craniofacial and central nervous system development such as MID1, NLGN4X, AMELX, ARHGAP6, and TBL1X. The whole clinical features of our proband possibly represents an unusual MLS syndromic phenotype caused by an Xp22.3p22.2 continuous gene deletion.
Effects of aligned electrospun fibers with different diameters on hemocompatibility, cell behaviors and inflammation in vitro
Authors: Yu Chenglong , Xing Meiyi , Wang Lu , Guan Guoping 
Published: January 2020

Abstract
An endothelial cell (EC) monolayer aligned along the direction of blood flow in vivo shows excellent capacity for anti-inflammation and anti-thrombosis. Therefore, aligned electrospun fibers have been much studied in the field of vascular implants since they are considered to facilitate the formation of an aligned EC monolayer, yet few research studies have been comprehensively reported concerning the effects of diameter scales of aligned fibers. In the present work, a series of aligned polycaprolactone (PCL) electrospun fibers with varying diameters ranging from dozens of nanometers to several micrometers were developed, and the effects of the fiber scales on EC behaviors, hemocompatibility as well as inflammatory cell behaviors were investigated, to evaluate their potential performance in the field of vascular implants. Our results showed that platelets exhibited small attachment forces on all fibers, and the anticoagulation property improved with the decrease of the fiber diameters. The impact of fiber diameters on human umbilical vein endothelial cell (HUVEC) adhesion and NO release was limited, while significant on HUVEC proliferation. With the increase of the fiber diameters, the elongation of HUVECs on our samples increased first then decreased, and exhibited maximum elongation degrees on 2738 nm and 2036 nm due to the strong contact guidance effect on these graphical cues; too thick or too fine fibers would weaken the contact guidance effect. Furthermore, we hypothesized that HUVECs cultured on 2036 nm had the smallest spreading area because of their elongation, but 2738 nm restricted HUVECs spreading limitedly. Similarly, NO production of HUVECs showed a similar change trend as their elongation degrees on different fibers. Except for 2036 nm, it exhibited the second highest NO production. For RAW 264.7 cells, poorer cell adhesion and lower TNF-α concentration of 1456 nm indicated its superior anti-inflammation property, while 73 nm showed a contrasting performance. Overall, these findings partly revealed the relationship between different topographies and cell behaviors, providing basic insight into vascular implant design.
Facile synthesis of corncob biochar via in-house modified pyrolysis for removal of methylene blue in wastewater
Authors: Suwunwong Thitipone , Hussain Naeem , Chantrapromma Suchada , Phoungthong Khamphe 
Published: January 2020

Abstract
Low-cost biochar was derived from corncob Zea mays L. cultivated in Northern Thailand for animal feed by facile synthesis with in-house modified pyrolysis for 2 h at ∼500 °C, ∼10 °C min−1 heating rate. Fixed-carbon, ash, %CHNSO and volatile contents of biochar were characterized and compared with pristine biomass. Thermal analysis was performed to monitor the transition of corncob biomass to biochar under the pyrolysis conditions. The physicochemical properties of biochar were investigated by scanning electron microscopy and FT-IR analysis, indicated honeycomb structure on the biochar surface with cylindrical pores and various functional groups, such as carbonyl and phenolic groups. Methylene blue adsorption in aqueous solution by biochar was studied at 25 °C. Without any chemical activation on biochar, the maximum removal efficiency of methylene blue by biochar was 16.50 mg g−1. Effect of the initial concentration and the contact time on removal of methylene blue was studied to archive optimal conditions. The equilibrium adsorption of methylene blue on the biochar was well fit by the Langmuir isotherm. Kinetic of adsorption was perfectly fit by a pseudo-second order dynamic model. The results suggest low-cost corncob biochar prepared by in-house modified pyrolysis could be utilized in wastewater treatment.
Effect of fiber orientation on dynamic mechanical properties of PALF hybridized with basalt reinforced epoxy composites
Authors: Doddi Parameswara Rao Venkata , Chanamala Ratnam , Dora Siva Prasad 
Published: January 2020

Abstract
In this modern era, the natural fibers usage in automobile and construction sectors has been increased. The goal of the current work was to investigate the fiber orientation effect on dynamic mechanical properties of hybrid Pineapple Leaf Fibre (PALF) hybridized with basalt reinforced epoxy composite at changing vibration frequencies. Hand Lay-up technique was used to manufacture the composites by keeping the unidirectional basalt fabric as an outer layer by keeping PALF as inner layer followed by static compression method. Tensile and flexural moduli were also determined apart from storage modulus (E′) and damping factor (tan δ) for different PALF fiber angles. The results exemplified that not only the storage modulus and loss factor but also glass transition temperature (Tg) as well found to increase with frequency and also the fiber orientation angle has a greater impact on dynamic and static properties.
Alternative Bi precursor effects on the structural, optical, morphological and photocatalytic properties of BiOI nanostructures
Authors: Florez-Rios J F , Santana-Aranda M A , Quiñones-Galván J G , Escobedo-Morales A , Chávez-Chávez A , Pérez-Centeno A 
Published: January 2020

Abstract
BiOI nanostructures were synthetized through a hydrothermal process using either bismuth acetate or subsalicylate as Bi precursor. Regardless of the used Bi source, the same crystalline structure of BiOI was obtained; nevertheless, the nature of the Bi precursor had an evident impact in the color appearance of the obtained sample. Another notable difference was observed in the resulting morphology, where ∼1.6 μm flower- and dandelion-like shapes were obtained for acetate and subsalicylate, respectively; both structures assembled by around 30 nm thick nanoflakes with rounded and straight edge, respectively. UV–vis diffuse reflectance shows an energy gap around 1.8 eV. Raman spectroscopy confirms also the tetragonal phase of BiOI. The photocatalytic activity was evaluated through degradation of methyl orange dye using visible and UV light sources, comparing results with P25 TiO2. Both BiOI nanostructures presented an improvement of photocatalytic activity when irradiated with visible light, having the best photoactivity the sample synthetized with bismuth acetate.
Opportunities for photonic integrated circuits in optical gas sensors
Authors: Hänsel Andreas , Heck Martijn J R 
Published: January 2020

Abstract
In this article, the potential of photonic integrated circuits (PICs) for modern gas sensing applications is discussed. Optical detection systems can be found at the high-end of the currently available gas detectors, and PIC-based optical spectroscopic devices promise a significant reduction in size and cost. The performance of such devices is reviewed here. This discussion is not limited to one semiconductor platform, but includes several available platforms operating from the visible wavelength range up to the long wavelength infrared. The different platforms are evaluated regarding their capabilities in creating a fully integrated spectroscopic setup, including light source, interaction cell and detection unit. Advanced spectroscopy methods are assessed regarding their PIC compatibility. Based on the comparison of PICs with state-of-the-art bulk optical devices, it can be concluded that they can fill the application space of compact and low cost optical gas sensors.
Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R
Authors: Anderson Warren D , Duarte Fabiana M , Civelek Mete , Guertin Michael J 
Published: January 2020

Abstract

Summary
Nascent transcript measurements derived from run-on sequencing experiments are critical for the investigation of transcriptional mechanisms and regulatory networks. However, conventional mRNA gene annotations significantly differ from the boundaries of primary transcripts. New primary transcript annotations are needed to accurately interpret run-on data. We developed the primaryTranscriptAnnotation R package to infer the transcriptional start and termination sites of primary transcripts from genomic run-on data. We then used these inferred coordinates to annotate transcriptional units identified de novo. This package provides the novel utility to integrate data-driven primary transcript annotations with transcriptional unit coordinates identified in an unbiased manner. Highlighting the importance of using accurate primary transcript coordinates, we demonstrate that this new methodology increases the detection of differentially expressed transcripts and provides more accurate quantification of RNA polymerase pause indices.

Availability and implementation
https://github.com/WarrenDavidAnderson/genomicsRpackage/tree/master/primaryTranscriptAnnotation.

Supplementary information
Supplementary data are available at Bioinformatics online.