bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lysine-specific demethylase 2A enhances binding of various nuclear factors to CpG-rich genomic DNAs by action of its CXXC-PHD domain
Authors: Iuchi Shiro , Paulo Joao A. 
Published: April 2019

AbstractThe lysine-specific demethylase 2A gene (KDM2A) is ubiquitously expressed and its transcripts consist of several alternatively spliced forms, including KDM2A and the shorter form N782 that lacks the 3′ end encoding F-box and LRR. KDM2A binds to numerous CpG-rich genomic loci and regulates various cellular activities; however, the mechanism of the pleiotropic function is unknown. Here, we identify the mechanism of KDM2A played by its CXXC-PHD domain. KDM2A is necessary for a rapid proliferation of post-natal keratinocytes while its 3′ end eclipses the stimulatory effect. EGFP-N782 binds to chromatin together with the XRCC5/6 complex, and the CXXC-PHD domain regulates the CpG-rich IGFBPL1 promoter. In vitro, CXXC-PHD enhances binding of nuclear extract ORC3 to the CpG-rich promoter, but not to the AT-rich DIP2B promoter to which ORC3 binds constitutively. Furthermore, CXXC-PHD recruits 94 nuclear factors involved in replication, ribosome synthesis, and mitosis, including POLR1A to the IGFBPL1 promoter. This recruitment is unprecedented; however, the result suggests that these nuclear factors bind to their cognate loci, as substantiated by the result that CXXC-PHD recruits POLR1A to the rDNA promoter. We propose that CXXC-PHD promotes permissiveness for nuclear factors to interact, but involvement of the XRCC5/6 complex in the recruitment is undetermined.
Eutectic modification by ternary compound cluster formation in Al-Si alloys
Authors: Barrirero J. , Pauly C. , Engstler M. , Ghanbaja J. , Ghafoor N. , Li J. , Schumacher P. , Odén M. , Mücklich F. 
Published: April 2019

AbstractAl-alloys with Si as the main alloying element constitute the vast majority of Al castings used commercially today. The eutectic Si microstructure in these alloys can be modified from plate-like to coral-like by the addition of a small amount of a third element to improve ductility and toughness. In this investigation the effects of Eu and Yb are studied and their influence on the microstructure is compared to further understand this modification. The two elements impact the alloy differently, where Eu modifies Si into a coral-like structure while Yb does not. Atom probe tomography shows that Eu is present within the Si phase in the form of ternary compound Al2Si2Eu clusters, while Yb is absent in the Si phase. This indicates that the presence of ternary compound clusters within Si is a necessary condition for the formation of a coral-like structure. A crystallographic orientation relationship between Si and the Al2Si2Eu phase was found, where the following plane normals are parallel: 011Si//0001Al2Si2Eu, 111Si//6$$\bar{7}$$

7
¯

10Al2Si2Eu and 011Si//6$$\bar{7}$$

7
¯

10Al2Si2Eu. No crystallographic relationship was found between Si and Al2Si2Yb. The heterogeneous formation of coherent Al2Si2Eu clusters inside the Si-phase is suggested to trigger the modification of the microstructure.
Autophagy is a new protective mechanism against the cytotoxicity of platinum nanoparticles in human trophoblasts
Authors: Nakashima Akitoshi , Higashisaka Kazuma , Kusabiraki Tae , Aoki Aiko , Ushijima Akemi , Ono Yosuke , Tsuda Sayaka , Shima Tomoko , Yoshino Osamu , Nagano Kazuya , Yoshioka Yasuo , Tsutsumi Yasuo , Saito Shigeru 
Published: April 2019

AbstractNanoparticles are widely used in commodities, and pregnant women are inevitably exposed to these particles. The placenta protects the growing fetus from foreign or toxic materials, and provides energy and oxygen. Here we report that autophagy, a cellular mechanism to maintain homeostasis, engulfs platinum nanoparticles (nPt) to reduce their cytotoxicity in trophoblasts. Autophagy was activated by nPt in extravillous trophoblast (EVT) cell lines, and EVT functions, such as invasion and vascular remodeling, and proliferation were inhibited by nPt. These inhibitory effects by nPt were augmented in autophagy-deficient cells. Regarding the dynamic state of nPt, analysis using ICP-MS demonstrated a higher accumulation of nPt in the autophagosome-rich than the cytoplasmic fraction in autophagy-normal cells. Meanwhile, there were more nPt in the nuclei of autophagy-deficient cells, resulting in greater DNA damage at a lower concentration of nPt. Thus, we found a new protective mechanism against the cytotoxicity of nPt in human trophoblasts.
Oxidation destabilizes toxic amyloid beta peptide aggregation
Authors: Razzokov J. , Yusupov M. , Bogaerts A. 
Published: April 2019

AbstractThe aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease.
Efficient Low Shear Flow-based Trapping of Biological Entities
Authors: Sohrabi Kashani Ahmad , Packirisamy Muthukumaran 
Published: April 2019

AbstractCapturing cells or biological entities is an important and challenging step toward in-vitro studies of cells under a precisely controlled microscale environment. In this work, we have developed a compact and efficient microdevice for on-chip trapping of micro-sized particles. This hydrodynamics-based trapping system allows the isolation of polystyrene micro-particles with a shorter time while inducing a less hydrodynamic deformation and stress on the particles or cells both after and before trapping. A numerical simulation was carried out to design a hydrodynamic trapping mechanism and optimize the geometric and fluidic parameters affecting the trapping efficiency of the microfluidic network. By using the finite element analysis, the velocity field, pressure field, and hydrodynamic force on the micro particles were studied. Finally, a PDMS microfluidic device was fabricated to test the device’s ability to trap polystyrene microspheres. Computational fluid analysis and experimental testing showed a high trapping efficiency that is more than 90%. This microdevice can be used for single cell studies including their biological, physical and chemical characterization.
Synergic effect of adsorbed gas and charging on surface flashover
Authors: Li Shengtao , Huang Yin , Min Daomin , Qu Guanghao , Niu Huan , Li Zhen , Wang Weiwang , Li Jianying , Liu Wenfeng 
Published: April 2019

AbstractFlashover is a crucial issue in both high-voltage engineering and surface physics. It not only challenges the existing theories about its dynamic evolution, but also inhibits the clean energy revolution by limiting the accessible voltage rating of power equipment. It is of significance to elucidate the microscopic process along the interface to improve the flashover performance. In the present study, the synergic effect of adsorbed gas and surface charging is investigated, which reveals a long ignored factor for determining the flashover voltage. Depending on the relative amount of adsorbed gas, the flashover voltage varies, which exhibit different behavior from the bulk breakdown of the same gas. The amount of N2 gas adsorbed on epoxy resin (EP) surface is much larger than that on Al2O3 ceramic surface, corresponding to the observed higher flashover voltage on EP. It is proposed that the adsorbed gas molecules not only modify the local surface charging state via their interaction with the trapped charges, but also capture free electrons due to the distortion of their electronic distribution. Both effects suppress the free path length of electrons in the gas-solid interface. This work explores another possibility to improve the surface flashover performance.
New marking method involving a light-emitting diode and power source device to localize gastrointestinal cancer in laparoscopic surgery
Authors: Wada Yuma , Miyoshi Norikatsu , Fujino Shiki , Ohue Masayuki , Yasui Masayoshi , Takahashi Yusuke , Takahashi Hidekazu , Nishimura Junichi , Takenaka Yuya , Saso Kazuhiro , Tomokuni Akira , Sugimura Keijiro , Akita Hirofumi , Takahashi Hidenori , Kobayashi Shogo , Omori Takeshi , Miyata Hiroshi , Yano Masahiko 
Published: April 2019

AbstractAlthough the preoperative endoscopic marking method using dye is widely used, the dye can spread into the tissue or abdominal cavity, inducing the inflammation and leading to the wrong dissection. We developed a novel marking method using an endoscopic clip with a light emitting diode (LED) and a power source device to detect the accurate location of the site of interest. We performed this new marking method in three patients with gastrointestinal cancers. We placed an endoscopic clip with an LED on the gastrointestinal mucosa and used a power source device outside of the human body to detect the LED. We detected the clip with the LED using the power source device. We also confirmed the usefulness of this clip in three of three (100%) patients with colorectal and gastric cancer. We developed a novel marking device using an LED to identify an objective location successfully.
A plasma protein derived TGFβ signature is a prognostic indicator in triple negative breast cancer
Authors: Katayama Hiroyuki , Tsou Peiling , Kobayashi Makoto , Capello Michela , Wang Hong , Esteva Francisco , Disis Mary L. , Hanash Samir 
Published: April 2019

AbstractWe investigated the potential of in-depth quantitative plasma proteome analysis to uncover proteins predictive of progression and metastasis in triple negative breast cancer (TNBC). Analysis of samples from 24 pre-menopausal and 24 post-menopausal women with newly diagnosed TNBC who subsequently developed metastasis or remained metastasis free were utilized in the proteomic discovery set, which resulted in 43 proteins associated with tumor progression. These proteins were found to form a hierarchical network with TGFβ. The signature was further confirmed and refined by integrating plasma protein data from a murine TNBC model that encompassed mice with rapid- versus slow-growing tumors. Three genes consisting of CLIC1, MAPRE1, and SERPINA3 in the refined TGFβ signature significantly stratified overall survival (log-rank p = 0.0141) in a larger validation cohort irrespective of menopausal status, tumor stage, grade, and size.
Chemical fixation of carbon dioxide catalyzed via cobalt (III) ONO pincer ligated complexes
Authors: Ullah Habib , Mousavi Bibimaryam , Younus Hussein A. , Khattak Zafar A. K. , Chaemchuen Somboon , Suleman Suleman , Verpoort Francis 
Published: April 2019

AbstractChemical insertion of carbon dioxide into epoxides under ambient conditions has become one of the most important methods for the construction of cyclic organic carbonates. Various active salen, salophen, and phenolate ligand based complexes have been reported for the synthesis of cyclic organic carbonates. Here we demonstrate a series of ONO pincer type cobalt (III) complexes as efficient catalysts for the cycloaddition of carbon dioxide to epoxides in neat conditions at atmospheric pressure with and without co-catalyst. A turnover number of up to 200,000 under atmospheric pressure is achieved. Moreover, the in situ generated complex shows high activity and the catalyst can be reused for at least 11 cycles without any decline in catalytic performance.
Gut microbiota in obstructive sleep apnea–hypopnea syndrome: disease-related dysbiosis and metabolic comorbidities
Authors: Ko Chih-Yuan , Liu Qing-Quan , Su Huan-Zhang , Zhang Hua-Ping , Fan Ji-Mim , Yang Jiao-Hong , Hu An-Ke , Liu Yu-Qi , Chou Dylan , Zeng Yi-Ming 
Published: April 2019

Abstract
Gut microbiota alterations manifest as intermittent hypoxia and fragmented sleep, thereby mimicking obstructive sleep apnea–hypopnea syndrome (OSAHS). Here, we sought to perform the first direct survey of gut microbial dysbiosis over a range of apnea–hypopnea indices (AHI) among patients with OSAHS. We obtained fecal samples from 93 patients with OSAHS [5 &lt; AHI ≤ 15 (n=40), 15 &lt; AHI ≤ 30 (n=23), and AHI ≥ 30 (n=30)] and 20 controls (AHI ≤ 5) and determined the microbiome composition via 16S rRNA pyrosequencing and bioinformatics analysis of variable regions 3–4. We measured fasting levels of homocysteine (HCY), interleukin-6 (IL-6), and tumor necrosis factor α (TNF-α). Results revealed gut microbial dysbiosis in several patients with varying severities of OSAHS, reliably separating them from controls with a receiver operating characteristic-area under the curve (ROC-AUC) of 0.789. Functional analysis in the microbiomes of patients revealed alterations; additionally, decreased in short-chain fatty acid (SCFA)-producing bacteria and increased pathogens, accompanied by elevated levels of IL-6. Lactobacillus levels correlated with HCY levels. Stratification analysis revealed that the Ruminococcus enterotype posed the highest risk for patients with OSAHS. Our results show that the presence of an altered microbiome is associated with HCY among OSAHS patients. These changes in the levels of SCFA affect the levels of pathogens that play a pathophysiological role in OSAHS and related metabolic comorbidities.
Emerging CRISPR/Cas9 applications for T-cell gene editing
Authors: Preece Roland , Georgiadis Christos 
Published: April 2019

Abstract
Gene editing tools are being rapidly developed, accelerating many areas of cell and gene therapy research. Each successive gene editing technology promises increased efficacy, improved specificity, reduced manufacturing cost and design complexity; all of which are currently epitomised by the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas9) platform. Since its conceptualisation, CRISPR-based gene editing has been applied to existing methodologies and has further allowed the exploration of novel avenues of research. Implementation of CRISPR/Cas9 has been instrumental to recent progress in the treatment of cancer, primary immunodeficiency, and infectious diseases. To this end, T-cell therapies have attempted to harness and redirect antigen recognition function, and through gene editing, broaden T-cell targeting capabilities and enhance their potency. The purpose of this review is to provide insights into emerging applications of CRISPR/Cas9 in T-cell therapies, to briefly address concerns surrounding CRISPR-mediated indel formation, and to introduce CRISPR/Cas9 base editing technologies that hold vast potential for future research and clinical translation.
Modeling of CoRoT and Spitzer lightcurves in NGC 2264 caused by an optically thick warp
Authors: Nagel E. , Bouvier J. 
Published: April 2019

Aims. We present an analysis of simultaneously observed CoRoT and Spitzer lightcurves for four systems in the stellar forming region NGC 2264: Mon-660, Mon-811, Mon-1140, and Mon-1308. These objects share in common a strong resemblance between the optical and infrared lightcurves, such that the mechanism responsible for producing them is the same. The aim of this paper is to explain both lightcurves simultaneously with only one mechanism.
Methods. We modeled the infrared emission as coming from a warp composed of an optically thick wall and an optically thick asymmetric disk beyond this location. We modeled the optical emission mainly by partial stellar occultation by the warp.
Results. The magnitude amplitude of the CoRoT and Spitzer observations for all the objects can be described with the emission coming from the system components. The difference between them is the value of the disk flux compared with the wall flux and the azimuthal variations of the former. This result points out the importance of the hydrodynamical interaction between the stellar magnetic field and the disk.
Conclusions. CoRoT and Spitzer lightcurves for the stellar systems Mon-660, Mon-811, Mon-1140, and Mon-1308 can be simultaneously explained using the emission coming from an asymmetric disk and emission with stellar occultation by an optically thick wall.
Destruction of dimethyl ether and methyl formate by collisions with He+
Authors: Ascenzi Daniela , Cernuto Andrea , Balucani Nadia , Tosi Paolo , Ceccarelli Cecilia , Martini Luca Matteo , Pirani Fernando 
Published: April 2019

Context. To correctly model the abundances of interstellar complex organic molecules (iCOMs) in different environments, both formation and destruction routes should be appropriately accounted for. While several scenarios have been explored for the formation of iCOMs via grain and gas-phase processes, much less work has been devoted to understanding the relevant destruction pathways, with special reference to (dissociative) charge exchange or proton transfer reactions with abundant atomic and molecular ions such as He+, H3+and HCO+.Aims. By using a combined experimental and theoretical methodology we provide new values for the rate coefficients and branching ratios (BRs) of the reactions of He+ions with two important iCOMs, namely dimethyl ether (DME) and methyl formate (MF). We also review the destruction routes of DME and MF by other two abundant ions, namely H3+and HCO+.Methods. Based on our recent laboratory measurements of cross sections and BRs for the DME/MF + He+reactions over a wide collision energy, we extended our theoretical insights on the selectivity of the microscopic dynamics to calculate the rate coefficientsk(T) in the temperature range from 10 to 298 K. We implemented these new and revised kinetic data in a general model of cold and warm gas, simulating environments where DME and MF have been detected.Results. Due to stereodynamical effects present at low collision energies, the rate coefficients, BRs and temperature dependences here proposed differ substantially from those reported in KIDA and UDfA, two of the most widely used astrochemical databases. These revised rates impact the predicted abundances of DME and MF, with variations up to 40% in cold gases and physical conditions similar to those present in prestellar cores.Conclusions. This work demonstrates that the accuracy of astrochemical models can be improved by a thorough characterisation of the destruction routes of iCOMs. The details of the chemical systems can, indeed, strongly affect their efficiency and significant deviations with respect to the commonly used Langevin model estimates are possible.
Nonconservative Rayleigh scattering
Authors: Frisch H. 
Published: April 2019

Context. The continuous spectrum of stellar and planetary atmospheres can be linearly polarized by Rayleigh or Thomson scattering. The polarization rate depends on the ratio κc/(κc + σc), κc and σc being the absorption coefficients due to photo-ionizations and scattering processes, respectively. The scattering process is conservative if κc = 0, and in this case the center-to-limb variation of the polarization rate follows Chandrasekhar’s law. Deviations from this law appear if the scattering is nonconservative, that is, if photons have a probability ϵ = κc/(κc + σc) of being destroyed at each scattering.
Aims. Nonconservative Rayleigh scattering is addressed here with a perturbation point of view, using ϵ, assumed to be a constant, as an expansion parameter. The goal is to obtain a perturbation expansion of the polarized radiation field that can be used to measure of the effects of a nonzero ϵ on the polarization rate of the emergent radiation and to check the accuracy of numerical codes.
Methods. The expansion method is an application to Rayleigh scattering of a general perturbation approach developed for scalar monochromatic transport equations. The introduction of a space variable, rescaled by a factor √ϵ, transforms the radiative transfer equation into a new equation from which one can extract simpler equations to describe the field in the interior of the medium and in boundary layers.
Results. The perturbation method is applied to a plane-parallel slab with no incident radiation and an unpolarized primary source of photons. The interior and boundary layer fields are expanded in powers of √ϵ. The expansion of the interior radiation field shows that it is unpolarized at leading order, with an intensity i0(τ̃) satisfying a diffusion equation, and that the polarization appears at order ϵ. The emergent radiation is calculated up to and including order ϵ. The leading term yields the polarization rate of the Chandrasekhar’s law. The following one, of order √ϵ, accurately predicts the decrease of the polarization rate for values of ϵ up to 10−3 and shows that it varies roughly as (1 − μ) for any unpolarized primary source. Methods for testing the accuracy of numerical schemes are proposed. The perturbation method is also applied to a slab with an incident radiation field and a polarized primary source of photons.
Modeling the e-APD SAPHIRA/C-RED ONE camera at low flux level
Authors: Lanthermann C. , Anugu N. , Le Bouquin J.-B. , Monnier J. D. , Kraus S. , Perraut K. 
Published: April 2019

Context. We implement an electron avalanche photodiode (e-APD) in the MIRC-X instrument, which is an upgrade of the six-telescope near-infrared imager MIRC, at the CHARA array. This technology should improve the sensitivity of near-infrared interferometry.
Aims. We aim to characterize a near-infrared C-RED ONE camera from First Light Imaging (FLI) using an e-APD from Leonardo (previously SELEX).
Methods. We first used the classical mean-variance analysis to measure the system gain and the amplification gain. We then developed a physical model of the statistical distribution of the camera output signal. This model is based on multiple convolutions of the Poisson statistic, the intrinsic avalanche gain distribution, and the observed distribution of the background signal. At low flux level, this model independently constrains the incident illumination level, the total gain, and the excess noise factor of the amplification.
Results. We measure a total transmission of 48 ± 3% including the cold filter and the Quantum Efficiency. We measure a system gain of 0.49 ADU/e, a readout noise of 10 ADU, and amplification gains as high as 200. These results are consistent between the two methods and therefore validate our modeling approach. The measured excess noise factor based on the modeling is 1.47 ± 0.03, with no obvious dependency with flux level or amplification gain.
Conclusions. The presented model allows the characteristics of the e-APD array to be measured at low flux level independently of a preexisting calibration. With < 0.3 electron equivalent readout noise at kilohertz frame rates, we confirm the revolutionary performances of the camera with respect to the PICNIC or HAWAII technologies. However, the measured excess noise factor is significantly higher than what is claimed in the literature (< 1.25), and explains why counting multiple photons remains challenging with this camera.