bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Inconsistent ROTI Derived From Multiconstellation GNSS Measurements of Globally Distributed GNSS Receivers for Ionospheric Irregularities Characterization
Authors: Liu Zhizhao , Yang Zhe , Xu Dongyang , Morton Y. Jade 
Published: February 2019

AbstractThis study for the first time presents an investigation into the exploitation of multi‐Global Navigation Satellite System (GNSS) observations (Global Positioning System, Globalnaya Navigazionnaya Sputnikovaya Sistema, Galileo, and BeiDou) to characterize ionospheric plasma irregularities, based on the rate of change of total electron content index (ROTI) sampled at 1 s. It is demonstrated that the multi‐GNSS ROTIs can represent temporal evolutions of ionospheric plasma irregularities during a large geomagnetic storm. However, an inconsistency in the magnitudes of multi‐GNSS ROTIs is found among a variety of GNSS receivers (i.e., Javad, Leica, Trimble, and Septentrio). Through cross comparisons between GNSS receivers installed at zero/short baselines and validations by receivers distributed separately, it is observed that the magnitude of ROTI corresponding to each system differs between closely installed and even collocated receivers of different models, as well as between the GNSS signals on the same frequency. From 1‐year (i.e., 2015) data analysis, it is found that the magnitudes of multi‐GNSS ROTIs exhibit the dependence on the receiver type. Among the four GNSS receiver types, the largest discrepancy in the multi‐GNSS ROTIs is observed from Septentrio receivers, while the smallest one is shown by Trimble receivers. A one‐to‐one comparison indicates that the ROTI difference is noticeable and can increase to 4–6 TECu/min under ionospheric irregularities conditions, that is, in the postsunset period of 18–02 local time. To investigate the inconsistency, the effect of adopting different equivalent noise bandwidths in the tracking loop design is discussed, via cross comparisons between a GNSS software‐defined receiver and a collocated Septentrio receiver. The result shows that adopting 15‐ and 2‐Hz noise bandwidths in the tracking loop can cause 0.2‐ to 0.5‐TECu/min differences in the magnitude of ROTI, suggesting that the diverse tracking techniques deployed by various receivers are very likely a major contributor to the inconsistency of multi‐GNSS ROTIs.
Thermochronological Evidence of Early Orogenesis, Eastern Pyrenees, France
Authors: Ternois Sébastien , Odlum Margaret , Ford Mary , Pik Raphaël , Stockli Daniel , Tibari Bouchaïb , Vacherat Arnaud , Bernard Vincent 
Published: February 2019

AbstractIn collisional orogens, distinguishing the thermal signature of early orogenesis from the preceding rift or from subsequent thermal events is a major challenge. We present an integrated geological and low‐temperature thermochronology study of the Paleozoic Agly‐Salvezines crustal block in the retrowedge of the eastern Pyrenees (France). The northern Pyrenees preserves one of the best geological records of a rift‐to‐collision transition. The Agly‐Salvezines block represents the inverted distal European margin of an Aptian–Cenomanian rift system. Seventeen samples were collected throughout the external orogenic massif and analyzed for low‐temperature thermochronology: zircon (U‐Th)/He dating documents the cooling history of the massif during the initiation and early phase of Pyrenean convergence, while apatite (U‐Th)/He dating completes the record of plate collision. Using inverse and forward modeling of new low‐temperature thermochronology data, we show that the Pyrenean retrowedge records two clear phases of orogenic cooling, Late Campanian–Maastrichtian and Ypresian–Bartonian, which we relate to early inversion of the distal rifted margin and main collision, respectively. An earlier, late Aptian–Turonian cooling history is detected, possibly related to rifting and/or postrift. No cooling is evidenced during the Paleocene during which tectonic quiescence is recorded in the adjacent Aquitaine retroforeland basin. Using our low‐temperature thermochronology data and geological constraints, we propose a crustal‐scale sequentially restored model for the tectonic and thermal transition from extension to peak orogenesis in the eastern Pyrenees, which suggests that both thrusting and underplating processes contributed to early inversion of the Aptian–Cenomanian rift system.
RETRACTED ARTICLE: Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi
Authors: Wu Baojun , Gaskell Jill , Zhang Jiwei , Toapanta Christina , Ahrendt Steven , Grigoriev Igor V , Blanchette Robert A , Schilling Jonathan S , Master Emma , Cullen Daniel , Hibbett David S 
Published: February 2019

Abstract
Fungi that decay wood have characteristic associations with certain tree species, but the mechanistic bases for these associations are poorly understood. We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the ‘Antrodia clade’ (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce, and aspen) in submerged cultures. We identified dozens to hundreds of substrate-biased genes (i.e., genes that are significantly upregulated in one substrate relative to the other two substrates) in each species, and these biased genes are correlated with their host ranges. Evolution of substrate-biased genes is associated with gene family expansion, gain and loss of genes, and variation in cis- and trans- regulatory elements, rather than changes in protein coding sequences. We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment. Moreover, we found that substrates could affect editing positions and frequency, including editing events occurring in mRNA transcribed from wood-decay-related genes. This work shows the extent to which gene expression and RNA editing differ among species and substrates, and provides clues into mechanisms by which wood-decaying fungi may adapt to different hosts.
DAP5 increases axonal outgrowth of hippocampal neurons by enhancing the cap-independent translation of DSCR1.4 mRNA
Authors: Seo Ji-Young , Jung Youngseob , Kim Do-Yeon , Ryu Hye Guk , Lee Juhyun , Kim Sung Wook , Kim Kyong-Tai 
Published: February 2019

AbstractProper wiring between neurons is indispensable for proper brain function. From the early developmental stage, axons grow and navigate to connect to targets according to specific guidance cues. The accuracy of axonal outgrowth and navigation are controlled by a variety of genes, and mutations and/or deficiencies in these genes are closely related to several brain disorders, such as autism. DSCR1 is one of these genes and regulates actin filament formation in axons. Thus, identifying the detailed regulatory mechanisms of DSCR1 expression is crucial for the understanding of the axon development of neurons; however, these regulatory mechanisms of DSCR1 remain unknown. Here, we discovered that mRNA encoding the DSCR1 isoform DSCR1.4 is present and mainly translated by the cap-independent initiation mechanisms in both the soma and axons of hippocampal neurons. We found that translation of DSCR1.4 mRNA is enhanced by death-associated protein 5 (DAP5), which can bind to DSCR1.4 5′UTR. BDNF-stimulus induced an increase in DAP5 expression and the cap-independent translation efficiency of DSCR1.4 mRNA in axon as well as soma. Furthermore, we showed the importance of the cap-independent translation of DSCR1.4 on enhancement of DSCR1.4 expression by BDNF-stimulus and axonal outgrowth of hippocampal neurons. Our findings suggest a new translational regulatory mechanism for DSCR1.4 expressions and a novel function of DAP5 as a positive regulator of DSCR1.4 mRNA translation induced in soma and axon of hippocampal neurons.
β-arrestin-2 in PAR-1-biased signaling has a crucial role in endothelial function via PDGF-β in stroke
Authors: Kanki Hideaki , Sasaki Tsutomu , Matsumura Shigenobu , Yokawa Satoru , Yukami Toshiro , Shimamura Munehisa , Sakaguchi Manabu , Furuno Tadahide , Suzuki Takahiro , Mochizuki Hideki 
Published: February 2019

AbstractThrombin aggravates ischemic stroke and activated protein C (APC) has a neuroprotective effect. Both proteases interact with protease-activated receptor 1, which exhibits functional selectivity and leads to G-protein- and β-arrestin-mediated-biased signal transduction. We focused on the effect of β-arrestin in PAR-1-biased signaling on endothelial function after stroke or high-fat diet (HFD). Thrombin had a rapid disruptive effect on endothelial function, but APC had a slow protective effect. Paralleled by prolonged MAPK 42/44 signaling activation by APC via β-arrestin-2, a lower cleavage rate of PAR-1 for APC than thrombin was quantitatively visualized by bioluminescence video imaging. HFD-fed mice showed lower β-arrestin-2 levels and more severe ischemic injury. The expression of β-arrestin-2 in capillaries and PDGF-β secretion in HFD-fed mice were reduced in penumbra lesions. These results suggested that β-arrestin-2-MAPK-PDGF-β signaling enhanced protection of endothelial function and barrier integrity after stroke.
CDK4/6 inhibitors target SMARCA4-determined cyclin D1 deficiency in hypercalcemic small cell carcinoma of the ovary
Authors: Xue Yibo , Meehan Brian , Macdonald Elizabeth , Venneti Sriram , Wang Xue Qing D. , Witkowski Leora , Jelinic Petar , Kong Tim , Martinez Daniel , Morin Geneviève , Firlit Michelle , Abedini Atefeh , Johnson Radia M. , Cencic Regina , Patibandla Jay , Chen Hongbo , Papadakis Andreas I. , Auguste Aurelie , de Rink Iris , Kerkhoven Ron M. , Bertos Nicholas , Gotlieb Walter H. , Clarke Blaise A. , Leary Alexandra , Witcher Michael , Guiot Marie-Christine , Pelletier Jerry , Dostie Josée , Park Morag , Judkins Alexander R. , Hass Ralf , Levine Douglas A. , Rak Janusz , Vanderhyden Barbara , Foulkes William D. , Huang Sidong 
Published: February 2019

AbstractInactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodelling gene, underlie small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). To reveal its druggable vulnerabilities, we perform kinase-focused RNAi screens and uncover that SMARCA4-deficient SCCOHT cells are highly sensitive to the inhibition of cyclin-dependent kinase 4/6 (CDK4/6). SMARCA4 loss causes profound downregulation of cyclin D1, which limits CDK4/6 kinase activity in SCCOHT cells and leads to in vitro and in vivo susceptibility to CDK4/6 inhibitors. SCCOHT patient tumors are deficient in cyclin D1 yet retain the retinoblastoma-proficient/p16INK4a-deficient profile associated with positive responses to CDK4/6 inhibitors. Thus, our findings indicate that CDK4/6 inhibitors, approved for a breast cancer subtype addicted to CDK4/6 activation, could be repurposed to treat SCCOHT. Moreover, our study suggests a novel paradigm whereby critically low oncogene levels, caused by loss of a driver tumor suppressor, may also be exploited therapeutically.
Brain songs framework used for discovering the relevant timescale of the human brain
Authors: Deco Gustavo , Cruzat Josephine , Kringelbach Morten L. 
Published: February 2019

AbstractA key unresolved problem in neuroscience is to determine the relevant timescale for understanding spatiotemporal dynamics across the whole brain. While resting state fMRI reveals networks at an ultraslow timescale (below 0.1 Hz), other neuroimaging modalities such as MEG and EEG suggest that much faster timescales may be equally or more relevant for discovering spatiotemporal structure. Here, we introduce a novel way to generate whole-brain neural dynamical activity at the millisecond scale from fMRI signals. This method allows us to study the different timescales through binning the output of the model. These timescales can then be investigated using a method (poetically named brain songs) to extract the spacetime motifs at a given timescale. Using independent measures of entropy and hierarchy to characterize the richness of the dynamical repertoire, we show that both methods find a similar optimum at a timescale of around 200 ms in resting state and in task data.
The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism
Authors: Arimura Yasuhiro , Tachiwana Hiroaki , Takagi Hiroki , Hori Tetsuya , Kimura Hiroshi , Fukagawa Tatsuo , Kurumizaka Hitoshi 
Published: February 2019

AbstractCentromeric nucleosomes are composed of the centromere-specific histone H3 variant CENP-A and the core histones H2A, H2B, and H4. To establish a functional kinetochore, histone H4 lysine-20 (H4K20) must be monomethylated, but the underlying mechanism has remained enigmatic. To provide structural insights into H4K20 methylation, we here solve the crystal structure of a nucleosome containing an H3.1-CENP-A chimera, H3.1CATD, which has a CENP-A centromere targeting domain and preserves essential CENP-A functions in vivo. Compared to the canonical H3.1 nucleosome, the H3.1CATD nucleosome exhibits conformational changes in the H4 N-terminal tail leading to a relocation of H4K20. In particular, the H4 N-terminal tail interacts with glutamine-76 and aspartate-77 of canonical H3.1 while these interactions are cancelled in the presence of the CENP-A-specific residues valine-76 and lysine-77. Mutations of valine-76 and lysine-77 impair H4K20 monomethylation both in vitro and in vivo. These findings suggest that a CENP-A-mediated structural polymorphism may explain the preferential H4K20 monomethylation in centromeric nucleosomes.
Large orbital polarization in nickelate-cuprate heterostructures by dimensional control of oxygen coordination
Authors: Liao Zhaoliang , Skoropata Elizabeth , Freeland J. W. , Guo Er-Jia , Desautels Ryan , Gao Xiang , Sohn Changhee , Rastogi Ankur , Ward T. Zac , Zou Tao , Charlton Timothy , Fitzsimmons Michael R. , Lee Ho Nyung 
Published: February 2019

AbstractArtificial heterostructures composed of dissimilar transition metal oxides provide unprecedented opportunities to create remarkable physical phenomena. Here, we report a means to deliberately control the orbital polarization in LaNiO3 (LNO) through interfacing with SrCuO2 (SCO), which has an infinite-layer structure for CuO2. Dimensional control of SCO results in a planar-type (P–SCO) to chain-type (C–SCO) structure transition depending on the SCO thickness. This transition is exploited to induce either a NiO5 pyramidal or a NiO6 octahedral structure at the SCO/LNO interface. Consequently, a large change in the Ni d orbital occupation up to ~30% is achieved in P–SCO/LNO superlattices, whereas the Ni eg orbital splitting is negligible in C–SCO/LNO superlattices. The engineered oxygen coordination triggers a metal-to-insulator transition in SCO/LNO superlattices. Our results demonstrate that interfacial oxygen coordination engineering provides an effective means to manipulate the orbital configuration and associated physical properties, paving a pathway towards the advancement of oxide electronics.
Air-stable redox-active nanomagnets with lanthanide spins radical-bridged by a metal–metal bond
Authors: Liu Fupin , Velkos Georgios , Krylov Denis S. , Spree Lukas , Zalibera Michal , Ray Rajyavardhan , Samoylova Nataliya A. , Chen Chia-Hsiang , Rosenkranz Marco , Schiemenz Sandra , Ziegs Frank , Nenkov Konstantin , Kostanyan Aram , Greber Thomas , Wolter Anja U. B. , Richter Manuel , Büchner Bernd , Avdoshenko Stanislav M. , Popov Alexey A. 
Published: February 2019

AbstractEngineering intramolecular exchange interactions between magnetic metal atoms is a ubiquitous strategy for designing molecular magnets. For lanthanides, the localized nature of 4f electrons usually results in weak exchange coupling. Mediating magnetic interactions between lanthanide ions via radical bridges is a fruitful strategy towards stronger coupling. In this work we explore the limiting case when the role of a radical bridge is played by a single unpaired electron. We synthesize an array of air-stable Ln2@C80(CH2Ph) dimetallofullerenes (Ln2 = Y2, Gd2, Tb2, Dy2, Ho2, Er2, TbY, TbGd) featuring a covalent lanthanide-lanthanide bond. The lanthanide spins are glued together by very strong exchange interactions between 4f moments and a single electron residing on the metal–metal bonding orbital. Tb2@C80(CH2Ph) shows a gigantic coercivity of 8.2 Tesla at 5 K and a high 100-s blocking temperature of magnetization of 25.2 K. The Ln-Ln bonding orbital in Ln2@C80(CH2Ph) is redox active, enabling electrochemical tuning of the magnetism.
Efficient cross-trait penalized regression increases prediction accuracy in large cohorts using secondary phenotypes
Authors: Chung Wonil , Chen Jun , Turman Constance , Lindstrom Sara , Zhu Zhaozhong , Loh Po-Ru , Kraft Peter , Liang Liming 
Published: February 2019

AbstractWe introduce cross-trait penalized regression (CTPR), a powerful and practical approach for multi-trait polygenic risk prediction in large cohorts. Specifically, we propose a novel cross-trait penalty function with the Lasso and the minimax concave penalty (MCP) to incorporate the shared genetic effects across multiple traits for large-sample GWAS data. Our approach extracts information from the secondary traits that is beneficial for predicting the primary trait based on individual-level genotypes and/or summary statistics. Our novel implementation of a parallel computing algorithm makes it feasible to apply our method to biobank-scale GWAS data. We illustrate our method using large-scale GWAS data (~1M SNPs) from the UK Biobank (N = 456,837). We show that our multi-trait method outperforms the recently proposed multi-trait analysis of GWAS (MTAG) for predictive performance. The prediction accuracy for height by the aid of BMI improves fromR2 = 35.8% (MTAG) to 42.5% (MCP + CTPR) or 42.8% (Lasso + CTPR) with UK Biobank data.
A Predictive Model for Cochlear Implant Outcome in Children with Cochlear Nerve Deficiency
Authors: Han Jae Joon , Suh Myung-Whan , Park Moo Kyun , Koo Ja-Won , Lee Jun Ho , Oh Seung Ha 
Published: February 2019

AbstractThe outcome of cochlear implantation (CI) in patients with cochlear nerve deficiency (CND) is variable, resulting in a wide range of speech perception performance, from degrees of environmental sound perception to conversation without lip-reading. Twenty-five cochlear implantees with CND were enrolled retrospectively to determine the factors correlated with CI outcome in patients with CND and to develop a predictive model for CI outcome. CI outcome was evaluated using the Categories of Auditory Performance (CAP) score at 2 years after CI. Patients with negative auditory brainstem response (ABR) showed a significantly lower CAP score than those with positive ABR (2.5 ± 1.7, 4.8 ± 0.7; p = 0.001). The area ratio of vestibulocochlear nerve (VCN) to facial nerve (FN) at the cerebellopontine angle on magnetic resonance images was positively correlated with CI outcome (p < 0.001). With multiple regression analysis, a predictive equation accounting for 66% of variance of CAP score at 2 years after CI was $${\bf{deduced}}:{\bf{CAP}}\,{\bf{score}}{\boldsymbol{=}}{\bf{0.7}}{\boldsymbol{+}}{\bf{1.9}}{\boldsymbol{\ast }}{\boldsymbol{(}}{\bf{ABR}}{\boldsymbol{)}}{\boldsymbol{+}}{\bf{1.2}}{\boldsymbol{\ast }}(\frac{{\boldsymbol{V}}{\boldsymbol{C}}{\boldsymbol{N}}}{{\boldsymbol{F}}{\boldsymbol{N}}})$$
deduced
:
CAP

score
=
0.7
+
1.9
∗

(

ABR

)

+
1.2
∗

(

V
C
N

F
N

)

. We found that preoperative ABR and area ratio of VCN to FN at the cerebellopontine angle could predict CI outcome in patients with CND. Preoperative counselling based on our predictive model might be helpful to determine treatment modality for auditory rehabilitation and which ear to implant.
High-resolution experimental and computational electrophysiology reveals weak β-lactam binding events in the porin PorB
Authors: Bartsch Annika , Llabrés Salomé , Pein Florian , Kattner Christof , Schön Markus , Diehn Manuel , Tanabe Mikio , Munk Axel , Zachariae Ulrich , Steinem Claudia 
Published: February 2019

AbstractThe permeation of most antibiotics through the outer membrane of Gram-negative bacteria occurs through porin channels. To design drugs with increased activity against Gram-negative bacteria in the face of the antibiotic resistance crisis, the strict constraints on the physicochemical properties of the permeants imposed by these channels must be better understood. Here we show that a combination of high-resolution electrophysiology, new noise-filtering analysis protocols and atomistic biomolecular simulations reveals weak binding events between the β-lactam antibiotic ampicillin and the porin PorB from the pathogenic bacterium Neisseria meningitidis. In particular, an asymmetry often seen in the electrophysiological characteristics of ligand-bound channels is utilised to characterise the binding site and molecular interactions in detail, based on the principles of electro-osmotic flow through the channel. Our results provide a rationale for the determinants that govern the binding and permeation of zwitterionic antibiotics in porin channels.
An investigation into non-covalent functionalization of a single-walled carbon nanotube and a graphene sheet with protein G:A combined experimental and molecular dynamics study
Authors: Ebrahim-Habibi Mohammad-Bagher , Ghobeh Maryam , Mahyari Farzaneh Aghakhani , Rafii-Tabar Hashem , Sasanpour Pezhman 
Published: February 2019

AbstractInvestigation of non-covalent interaction of hydrophobic surfaces with the protein G (PrG) is necessary due to their frequent utilization in immunosensors and ELISA. It has been confirmed that surfaces, including carbonous-nanostructures (CNS) could orient proteins for a better activation. Herein, PrG interaction with single-walled carbon nanotube (SWCNT) and graphene (Gra) nanostructures was studied by employing experimental and MD simulation techniques. It is confirmed that the PrG could adequately interact with both SWCNT and Gra and therefore fine dispersion for them was achieved in the media. Results indicated that even though SWCNT was loaded with more content of PrG in comparison with the Gra, the adsorption of the PrG on Gra did not induce significant changes in the IgG tendency. Several orientations of the PrG were adopted in the presence of SWCNT or Gra; however, SWCNT could block the PrG-FcR. Moreover, it was confirmed that SWCNT reduced the α-helical structure content in the PrG. Reduction of α-helical structure of the PrG and improper orientation of the PrG-SWCNT could remarkably decrease the PrG tendency to the Fc of the IgG. Importantly, the Gra could appropriately orient the PrG by both exposing the PrG-FcR and also by blocking the fragment of the PrG that had tendency to interact with Fab in IgG.
Micro-Particle Operations Using Asymmetric Traps
Authors: Lee Jaesung , Mena Sarah E. , Burns Mark A. 
Published: February 2019

AbstractMicro-particle operations in many lab-on-a-chip devices require active-type techniques that are accompanied by complex fabrication and operation. The present study describes an alternative method using a passive microfluidic scheme that allows for simpler operation and, therefore, potentially less expensive devices. We present three practical micro-particle operations using our previously developed passive mechanical trap, the asymmetric trap, in a non-acoustic oscillatory flow field. First, we demonstrate size-based segregation of both binary and ternary micro-particle mixtures using size-dependent trap-particle interactions to induce different transport speeds for each particle type. The degree of segregation, yield, and purity of the binary segregations are 0.97 ± 0.02, 0.96 ± 0.06, and 0.95 ± 0.05, respectively. Next, we perform a solution exchange by displacing particles from one solution into another in a trap array. Lastly, we focus and split groups of micro-particles by exploiting the transport polarity of asymmetric traps. These operations can be implemented in any closed fluidic circuit containing asymmetric traps using non-acoustic oscillatory flow, and they open new opportunities to flexibly control micro-particles in integrated lab-on-a-chip platforms with minimal external equipment.