bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalized conditions of spherical carbonate concretion formation around decaying organic matter in early diagenesis
Authors: Yoshida Hidekazu , Yamamoto Koshi , Minami Masayo , Katsuta Nagayoshi , Sin-ichi Sirono , Metcalfe Richard 
Published: April 2018

AbstractIsolated spherical carbonate concretions observed in marine sediments are fascinating natural objet trouve because of their rounded shapes and distinct sharp boundaries. They occur in varied matrices and often contain well preserved fossils. The formation process of such concretions has been explained by diffusion and rapid syn-depositional reactions with organic solutes and other pore water constituents. However, the rates, conditions and formation process of syngenetic spherical concretions are still not fully clear. Based on the examination of different kinds of spherical concretions from several locations in Japan, a diffusion based growth diagram was applied to define the generalized growth conditions of spherical concretions formed around decaying organic matter. All analytical data imply that the spherical concretions formed very rapidly, at least three to four orders of magnitude faster than previously estimated timescales. The values indicate that spherical concretions are preferentially grown within clay- to silt-grade marine sediments deposited in relatively deep (a few tens of metres) environments dominated by diffusive solute transport, very early in diagenesis.
Extreme air pollution events in Hokkaido, Japan, traced back to early snowmelt and large-scale wildfires over East Eurasia: Case studies
Authors: Yasunari Teppei J. , Kim Kyu-Myong , da Silva Arlindo M. , Hayasaki Masamitsu , Akiyama Masayuki , Murao Naoto 
Published: April 2018

AbstractTo identify the unusual climate conditions and their connections to air pollutions in a remote area due to wildfires, we examine three anomalous large-scale wildfires in May 2003, April 2008, and July 2014 over East Eurasia, as well as how products of those wildfires reached an urban city, Sapporo, in the northern part of Japan (Hokkaido), significantly affecting the air quality. NASA’s MERRA-2 (the Modern-Era Retrospective analysis for Research and Applications, Version 2) aerosol re-analysis data closely reproduced the PM2.5 variations in Sapporo for the case of smoke arrival in July 2014. Results show that all three cases featured unusually early snowmelt in East Eurasia, accompanied by warmer and drier surface conditions in the months leading to the fires, inducing long-lasting soil dryness and producing climate and environmental conditions conducive to active wildfires. Due to prevailing anomalous synoptic-scale atmospheric motions, smoke from those fires eventually reached a remote area, Hokkaido, and worsened the air quality in Sapporo. In future studies, continuous monitoring of the timing of Eurasian snowmelt and the air quality from the source regions to remote regions, coupled with the analysis of atmospheric and surface conditions, may be essential in more accurately predicting the effects of wildfires on air quality.
Multifunctional activities of ERF109 as affected by salt stress in Arabidopsis
Authors: Bahieldin Ahmed , Atef Ahmed , Edris Sherif , Gadalla Nour O. , Ramadan Ahmed M. , Hassan Sabah M. , Al Attas Sanaa G. , Al-Kordy Magdy A. , Al-Hajar Abdulrahman S. M. , Sabir Jamal S. M. , Nasr Mahmoud E. , Osman Gamal H. , El-Domyati Fotouh M. 
Published: April 2018

AbstractTranscriptomic analysis was conducted in leaves of Arabidopsis T-DNA insertion ERF109-knocked out (KO) mutant or plants overexpressing (OE) the gene to detect its role in driving expression of programmed cell death- (PCD-) or growth-related genes under high salt (200 mM NaCl) stress. The analysis yielded ~22–24 million reads, of which 90% mapped to the Arabidopsis reference nuclear genome. Hierarchical cluster analysis of gene expression and principal component analysis (PCA) successfully separated transcriptomes of the two stress time points. Analysis indicated the occurrence of 65 clusters of gene expression with transcripts of four clusters differed at the genotype (e.g., WT (wild type), KO
ERF109
or OE
ERF109
) level. Regulated transcripts involved DIAP1-like gene encoding a death-associated inhibitor of reactive oxygen species (ROS). Other ERF109-regulated transcripts belong to gene families encoding ROS scavenging enzymes and a large number of genes participating in three consecutive pathways, e.g., phenylalanine, tyrosine and tryptophan biosynthesis, tryptophan metabolism and plant hormone signal transduction. We investigated the possibility that ERF109 acts as a “master switch” mediator of a cascade of consecutive events across these three pathways initially by driving expression of ASA1 and YUC2 genes and possibly driving GST, IGPS and LAX2 genes. Action of downstream auxin-regulator, auxin-responsive as well as auxin carrier genes promotes plant cell growth under adverse conditions.
Presence and User Experience in a Virtual Environment under the Influence of Ethanol: An Explorative Study
Authors: Lorenz Mario , Brade Jennifer , Diamond Lisa , Sjölie Daniel , Busch Marc , Tscheligi Manfred , Klimant Philipp , Heyde Christoph-E. , Hammer Niels 
Published: April 2018

AbstractVirtual Reality (VR) is used for a variety of applications ranging from entertainment to psychological medicine. VR has been demonstrated to influence higher order cognitive functions and cortical plasticity, with implications on phobia and stroke treatment. An integral part for successful VR is a high sense of presence – a feeling of ‘being there’ in the virtual scenario. The underlying cognitive and perceptive functions causing presence in VR scenarios are however not completely known. It is evident that the brain function is influenced by drugs, such as ethanol, potentially confounding cortical plasticity, also in VR. As ethanol is ubiquitous and forms part of daily life, understanding the effects of ethanol on presence and user experience, the attitudes and emotions about using VR applications, is important. This exploratory study aims at contributing towards an understanding of how low-dose ethanol intake influences presence, user experience and their relationship in a validated VR context. It was found that low-level ethanol consumption did influence presence and user experience, but on a minimal level. In contrast, correlations between presence and user experience were strongly influenced by low-dose ethanol. Ethanol consumption may consequently alter cognitive and perceptive functions related to the connections between presence and user experience.
Structural and kinetic basis for the selectivity of aducanumab for aggregated forms of amyloid-β
Authors: Arndt Joseph W. , Qian Fang , Smith Benjamin A. , Quan Chao , Kilambi Krishna Praneeth , Bush Martin W. , Walz Thomas , Pepinsky R. Blake , Bussière Thierry , Hamann Stefan , Cameron Thomas O. , Weinreb Paul H. 
Published: April 2018

AbstractAducanumab, a human-derived antibody targeting amyloid-β (Aβ), is in Phase 3 clinical trials for the treatment of Alzheimer’s disease. Biochemical and structural analyses show that aducanumab binds a linear epitope formed by amino acids 3–7 of the Aβ peptide. Aducanumab discriminates between monomers and oligomeric or fibrillar aggregates based on weak monovalent affinity, fast binding kinetics and strong avidity for epitope-rich aggregates. Direct comparative studies with analogs of gantenerumab, bapineuzumab and solanezumab demonstrate clear differentiation in the binding properties of these antibodies. The crystal structure of the Fab fragment of aducanumab bound to its epitope peptide reveals that aducanumab binds to the N terminus of Aβ in an extended conformation, distinct from those seen in structures with other antibodies that target this immunodominant epitope. Aducanumab recognizes a compact epitope that sits in a shallow pocket on the antibody surface.In silicoanalyses suggest that aducanumab interacts weakly with the Aβ monomer and may accommodate a variety of peptide conformations, further supporting its selectivity for Aβ aggregates. Our studies provide a structural rationale for the low affinity of aducanumab for non-pathogenic monomers and its greater selectivity for aggregated forms than is seen for other Aβ-targeting antibodies.
Development of new method to enrich human iPSC-derived renal progenitors using cell surface markers
Authors: Hoshina Azusa , Kawamoto Tatsuya , Sueta Shin-Ichi , Mae Shin-Ichi , Araoka Toshikazu , Tanaka Hiromi , Sato Yasunori , Yamagishi Yukiko , Osafune Kenji 
Published: April 2018

AbstractCell therapy using renal progenitors differentiated from human embryonic stem cells (hESCs) or induced pluripotent stem cells (hiPSCs) has the potential to significantly reduce the number of patients receiving dialysis therapy. However, the differentiation cultures may contain undifferentiated or undesired cell types that cause unwanted side effects, such as neoplastic formation, when transplanted into a body. Moreover, the hESCs/iPSCs are often genetically modified in order to isolate the derived renal progenitors, hampering clinical applications. To establish an isolation method for renal progenitors induced from hESCs/iPSCs without genetic modifications, we screened antibodies against cell surface markers. We identified the combination of four markers, CD9−CD140a+CD140b+CD271+, which could enrich OSR1+SIX2+ renal progenitors. Furthermore, these isolated cells ameliorated renal injury in an acute kidney injury (AKI) mouse model when used for cell therapy. These cells could contribute to the development of hiPSC-based cell therapy and disease modeling against kidney diseases.
Finite-time quantum entanglement in propagating squeezed microwaves
Authors: Fedorov K. G. , Pogorzalek S. , Las Heras U. , Sanz M. , Yard P. , Eder P. , Fischer M. , Goetz J. , Xie E. , Inomata K. , Nakamura Y. , Di Candia R. , Solano E. , Marx A. , Deppe F. , Gross R. 
Published: April 2018

AbstractTwo-mode squeezing is a fascinating example of quantum entanglement manifested in cross-correlations of non-commuting observables between two subsystems. At the same time, these subsystems themselves may contain no quantum signatures in their self-correlations. These properties make two-mode squeezed (TMS) states an ideal resource for applications in quantum communication. Here, we generate propagating microwave TMS states by a beam splitter distributing single mode squeezing emitted from distinct Josephson parametric amplifiers along two output paths. We experimentally study the fundamental dephasing process of quantum cross-correlations in continuous-variable propagating TMS microwave states and accurately describe it with a theory model. In this way, we gain the insight into finite-time entanglement limits and predict high fidelities for benchmark quantum communication protocols such as remote state preparation and quantum teleportation.
SRC-like adaptor protein 2 (SLAP2) is a negative regulator of KIT-D816V-mediated oncogenic transformation
Authors: Rupar Kaja , Moharram Sausan A. , Kazi Julhash U. , Rönnstrand Lars 
Published: April 2018

AbstractKIT is a receptor tyrosine kinase (RTK) involved in several cellular processes such as regulation of proliferation, survival and differentiation of early hematopoietic cells, germ cells and melanocytes. Activation of KIT results in phosphorylation of tyrosine residues in the receptor, and recruitment of proteins that mediate downstream signaling and also modulate receptor signaling. Here we show that the SRC-like adaptor protein 2 (SLAP2) binds to wild-type KIT in a ligand-dependent manner and is furthermore found constitutively associated with the oncogenic mutant KIT-D816V. Peptide fishing analysis mapped pY568 and pY570 as potential SLAP2 association sites in KIT, which overlaps with the SRC binding sites in KIT. Expression of SLAP2 in cells expressing the transforming mutant KIT-D816V led to reduced cell viability and reduced colony formation. SLAP2 also partially blocked phosphorylation of several signal transduction molecules downstream of KIT such as AKT, ERK, p38 and STAT3. Finally, SLAP2 expression enhanced ubiquitination of KIT and its subsequent degradation. Taken together, our data demonstrate that SLAP2 negatively modulates KIT-D816V-mediated transformation by enhancing degradation of the receptor.
Analysis of dynamically stable patterns in a maze-like corridor using the Wasserstein metric
Authors: Ishiwata Ryosuke , Kinukawa Ryota , Sugiyama Yuki 
Published: April 2018

AbstractThe two-dimensional optimal velocity (2d-OV) model represents a dissipative system with asymmetric interactions, thus being suitable to reproduce behaviours such as pedestrian dynamics and the collective motion of living organisms. In this study, we found that particles in the 2d-OV model form optimal patterns in a maze-like corridor. Then, we estimated the stability of such patterns using the Wasserstein metric. Furthermore, we mapped these patterns into the Wasserstein metric space and represented them as points in a plane. As a result, we discovered that the stability of the dynamical patterns is strongly affected by the model sensitivity, which controls the motion of each particle. In addition, we verified the existence of two stable macroscopic patterns which were cohesive, stable, and appeared regularly over the time evolution of the model.
Anisotropic magnetotransport and extremely large magnetoresistance in NbAs2 single crystals
Authors: Peramaiyan G. , Sankar Raman , Muthuselvam I. Panneer , Lee Wei-Li 
Published: April 2018

AbstractWe report the extremely large magnetoresistance and anisotropic magnetoresistance in a non-magnetic semimetallic NbAs2 single crystal. Unsaturated transverse XMR with quadratic field dependence has been observed to be ~3 × 105 % at 2 K and 15 T. Up to 12.5 K, clear Shubnikov de Haas (SdH) quantum oscillations were observed from which two distinct Fermi pockets were identified. The corresponding quantum electronic parameters such as effective cyclotron mass and Dingle temperature were obtained using Lifshitz-Kosevich formula. From the field dependent Hall resistivity at 2 K, carrier concentrations n
e
(n
h
) = 6.7691 (6.4352) × 1025 m−3 and mobilities μ
e
(μ
h
) = 5.6676 (7.6947) m2 V−1 s−1 for electrons (e) and holes (h) were extracted using semiclassical two-band model fitting. We observed large anisotropic magnetoresistance about 84%, 75%, and 12% at 0.75 T and 6 K for three different orientations γ, θ and ϕ, respectively, similar to that in several topological semimetallic systems. Magnetic properties of NbAs2 are similar to the case of graphite, without any phase transition in the temperature range from 5 K to 300 K.
Pivotal roles of Kupffer cells in the progression and regression of DDC-induced chronic cholangiopathy
Authors: Jemail Leila , Miyao Masashi , Kotani Hirokazu , Kawai Chihiro , Minami Hirozo , Abiru Hitoshi , Tamaki Keiji 
Published: April 2018

AbstractKupffer cells (KCs) are key players in maintaining tissue homeostasis and are involved in various liver diseases. However, the roles of KCs in the pathogenesis of cholangiopathy are largely unknown. We aimed to investigate the precise roles of KCs in both the progression and regression phases of the 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-induced cholangiopathy model. In the early phase of DDC-induced cholangiopathy, the number of KCs significantly increased over time. Moreover, KCs were associated with abnormal phenotypic changes in other liver cells, such as hepatocytes, biliary epithelial cells, liver sinusoidal endothelial cells, and hepatic stellate cells. In contrast, KC depletion by clodronate administration suppressed the progression of the disease, and maintained the phenotypes of other cells. In the regression phase, the numbers of KCs significantly decreased, and the cells redifferentiated to their quiescent state. In contrast, KC depletion delayed the recovery of cells by maintaining other liver cells in an active state. These findings suggest that KCs play detrimental roles in the progression phase; however, they are beneficial in the regression phase by mediating interactions between other liver cells. Our data provide new insights into the roles of KCs in the pathogenesis of cholangiopathy.
On the role of the prefrontal cortex in fatigue effects on cognitive flexibility - a system neurophysiological approach
Authors: Petruo Vanessa A. , Mückschel Moritz , Beste Christian 
Published: April 2018

AbstractDemanding tasks like cognitive flexibility show time-related deterioration of performance (i.e. fatigability effects). Fatigability has been associated with structural and functional properties of the prefrontal cortex. However, the electrophysiological underpinnings of these processes are not well understood. We examined n = 34 healthy participants with a task switching paradigm in which switches were either signaled by cues or needed to be maintained by working memory processes. We analyzed event-related potentials (ERPs) and performed residue iteration decomposition (RIDE) to account for effects of fatigue on intra-individual variability of neurophysiological data. This was combined with source localization methods. We show that task switching is affected by time on task (TOT) effects mostly when working memory processes are needed. On a neurophysiological level, this effect could not be observed in standard ERPs, but only after accounting for intra-individual variability using RIDE. The RIDE data suggests that during task switching, fatigability specifically affects response recoding processes that are associated with functions of the middle frontal gyrus (MFG; BA10). The results underline propositions of the ‘opportunity cost model’, which states that fatigability effects of executive functions depend on the degree to which tasks engage similar prefrontal regions - in this case working memory and task switching mechanisms.
Microscopic Description of the Ferroism in Lead-Free AlFeO3
Authors: Santos Guilherme M. , Catellani Igor B. , Santos Ivair A. , Guo Ruyan , Bhalla Amar S. , Padilha José Eduardo , Cótica Luiz F. 
Published: April 2018

AbstractThe microscopic origin of the ferroic and multiferroic properties of AlFeO3 have been carefully investigated. The maximum entropy method was applied to X-ray diffraction data and ab initio density functional theory calculations in order to obtain the electron density distributions and electric polarization. The study of chemical bonds shows that the bonds between Fe(3d) and O(2p) ions are anisotropic, leading to the configuration of shorter/longer and stronger/weaker bonds. This leads to electric polarization. Density of states calculations showed a magnetic polarization as a result of a weak ferromagnetic ordering. These results unambiguously show that AlFeO3 is a multiferroic material and exhibits a magnetoelectric coupling at room temperature, as has already been shown by experiments.
Electrochemical affinity biosensors for fast detection of gene-specific methylations with no need for bisulfite and amplification treatments
Authors: Povedano Eloy , Vargas Eva , Montiel Víctor Ruiz-Valdepeñas , Torrente-Rodríguez Rebeca M. , Pedrero María , Barderas Rodrigo , Segundo-Acosta Pablo San , Peláez-García Alberto , Mendiola Marta , Hardisson David , Campuzano Susana , Pingarrón José M. 
Published: April 2018

AbstractThis paper describes two different electrochemical affinity biosensing approaches for the simple, fast and bisulfite and PCR-free quantification of 5-methylated cytosines (5-mC) in DNA using the anti-5-mC antibody as biorecognition element. One of the biosensing approaches used the anti-5-mC as capture bioreceptor and a sandwich type immunoassay, while the other one involved the use of a specific DNA probe and the anti-5-mC as a detector bioreceptor of the captured methylated DNA. Both strategies, named for simplicity in the text as immunosensor and DNA sensor, respectively, were implemented on the surface of magnetic microparticles and the transduction was accomplished by amperometry at screen-printed carbon electrodes by means of the hydrogen peroxide/hydroquinone system. The resulting amperometric biosensors demonstrated reproducibility throughout the entire protocol, sensitive determination with no need for using amplification strategies, and competitiveness with the conventional enzyme-linked immunosorbent assay methodology and the few electrochemical biosensors reported so far in terms of simplicity, sensitivity and assay time. The DNA sensor exhibited higher sensitivity and allowed the detection of the gene-specific methylations conversely to the immunosensor, which detected global DNA methylation. In addition, the DNA sensor demonstrated successful applicability for 1 h-analysis of specific methylation in two relevant tumor suppressor genes in spiked biological fluids and in genomic DNA extracted from human glioblastoma cells.
Tau Internalization is Regulated by 6-O Sulfation on Heparan Sulfate Proteoglycans (HSPGs)
Authors: Rauch Jennifer N. , Chen John J. , Sorum Alexander W. , Miller Gregory M. , Sharf Tal , See Stephanie K. , Hsieh-Wilson Linda C. , Kampmann Martin , Kosik Kenneth S. 
Published: April 2018

AbstractThe misfolding and accumulation of tau protein into intracellular aggregates known as neurofibrillary tangles is a pathological hallmark of neurodegenerative diseases such as Alzheimer’s disease. However, while tau propagation is a known marker for disease progression, exactly how tau propagates from one cell to another and what mechanisms govern this spread are still unclear. Here, we report that cellular internalization of tau is regulated by quaternary structure and have developed a cellular assay to screen for genetic modulators of tau uptake. Using CRISPRi technology we have tested 3200 genes for their ability to regulate tau entry and identified enzymes in the heparan sulfate proteoglycan biosynthetic pathway as key regulators. We show that 6-O-sulfation is critical for tau-heparan sulfate interactions and that this modification regulates uptake in human central nervous system cell lines, iPS-derived neurons, and mouse brain slice culture. Together, these results suggest novel strategies to halt tau transmission.
MicroED structure of the NaK ion channel reveals a Na+ partition process into the selectivity filter
Authors: Liu Shian , Gonen Tamir 
Published: April 2018

AbstractSodium (Na+) is a ubiquitous and important inorganic salt mediating many critical biological processes such as neuronal excitation, signaling, and facilitation of various transporters. The hydration states of Na+ are proposed to play critical roles in determining the conductance and the selectivity of Na+ channels, yet they are rarely captured by conventional structural biology means. Here we use the emerging cryo-electron microscopy (cryoEM) method micro-electron diffraction (MicroED) to study the structure of a prototypical tetrameric Na+-conducting channel, NaK, to 2.5 Å resolution from nano-crystals. Two new conformations at the external site of NaK are identified, allowing us to visualize a partially hydrated Na+ ion at the entrance of the channel pore. A process of dilation coupled with Na+ movement is identified leading to valuable insights into the mechanism of ion conduction and gating. This study lays the ground work for future studies using MicroED in membrane protein biophysics.