bluuebunny/crossref_metadata_2025_split huggingface dataset:
Particle‐Based Modeling of Transtensional Pull‐Apart Basins
Authors: Liu Yuan , Konietzky Heinz 
Published: November 2018

AbstractScaled underlapping models based on the discrete element method are used to investigate crack propagation and basin development in transtensional systems with both parallel and nonparallel master faults. The introduction of a small component of oblique divergent motion causes the crack pattern and basin geometry to become quite different. The 5° transtensional model with parallel master faults produces a much wider depression separated by a cross‐basin fault, compared to pure strike slip. A single throughgoing fault that connects the two master faults forms when the obliquity of 10° is reached. For transtensional model with two nonparallel master faults, a minor change of one master fault from parallel to nonparallel with a small component of 5° causes the crack pattern to become much more diffuse. As the obliquity increases from 5° to 15°, the first cracks propagate at a higher angle relative to the master faults, the cross‐basin fault forms at a lower angle clockwise to the motion direction, and the area of the first depression decreases. A single throughgoing fault linking the two master faults initiates when the obliquity of 20° is obtained. The crack patterns and basin geometries of our numerical models show many similarities to natural transtensional basins including the Cinarcik Basin and the Central Basin in the Sea of Marmara. The transtensional models with various initial fault kinematics and different obliquities lead to different fault linkages, which has implications for the possible earthquake hazards in the Sea of Marmara near Istanbul.
Three‐Dimensional Architecture, Structural Evolution, and Role of Inheritance Controlling Detachment Faulting at a Hyperextended Distal Margin: The Example of the Err Detachment System (SE Switzerland)
Authors: Epin M.‐E. , Manatschal G. 
Published: November 2018

AbstractWhile extensional detachment systems linked to postorogenic or oceanic settings have been described from many places, examples linked to hyperextension and formation of magma‐poor rifted margins remain rare. Here we describe one of the best preserved examples of a detachment system that is exposed over 200 km2 in the Err nappe in SE Switzerland. Based on existing and new mapping, we realized a new map that enables to describe the 3‐D structure of a detachment system and its role in thinning the crust and controlling the architecture and structural evolution of a hyperextended margin. We show that the Err detachment system is formed by at least three in‐sequence detachment faults. The 3‐D architecture of these faults and of their hanging wall blocks is controlled by inherited structures and a prerift evaporite level. The geometrical relationships and the evolution of the detachment system show deviations from the classical rolling hinge model. From the observations it remains unclear how and where the detachment faults rooted at depth. The overall observations made in the Err nappe allow to describe how the final rift evolution preceding mantle exhumation can be explained by extensional detachment systems and how these structures shape the hyperextended continental wedge at distal margins. While these questions are difficult to answer at present‐day rifted margins, the use of a kilometer‐scale field analogue can help to upscale and to interpret extensional detachment systems at present‐day distal, magma‐poor rifted margins.
The role of convergent ion channel pathways in microglial phenotypes: a systematic review of the implications for neurological and psychiatric disorders
Authors: Quagliato Laiana A. , Nardi Antonio E. 
Published: November 2018

AbstractIncreases in the activated state of microglia, the main neuroimmune cells, are widely reported in the brains of patients with neurological and psychiatric disorders. Microglia transform from the resting to the activated state by sensing their environment, aided by a variety of ion channels. To examine the effect of ion channels on microglial phenotypes, we conducted a systematic review of immunohistochemical analyses of these neuroimmune cells in animal models following administration of ion channel antagonists, compared to control conditions. A systematic search of the PubMed and Web of Science electronic databases using the PRISMA and WHO methodologies for systematic reviews yielded 15 original peer-reviewed studies. The majority (13 out of 15) of these studies reported a decrease in microglial activated state after ion signaling pharmacological blockade. The studies provide evidence that acute administration of ion channel antagonists leads to a reduction in microglial activation in rodent brains in the models for epilepsy, Parkinson’s disease, inflammation, pain, ischemia, and brain and spinal cord injury. Future research should explore microglial-specific druggable targets for neurological and psychiatric disorders. The investigation of acute and chronic administration of ion channel antagonists in microglial phenotypes in primates and the development of microglia-like cells derived from human stem cells could be valuable sources in this direction.
Non-canonical nucleosides and chemistry of the emergence of life
Authors: Becker Sidney , Schneider Christina , Crisp Antony , Carell Thomas 
Published: November 2018

AbstractPrebiotic chemistry, driven by changing environmental parameters provides canonical and a multitude of non-canonical nucleosides. This suggests that Watson-Crick base pairs were selected from a diverse pool of nucleosides in a pre-Darwinian chemical evolution process.
Targeting the BRD4/FOXO3a/CDK6 axis sensitizes AKT inhibition in luminal breast cancer
Authors: Liu Jingyi , Duan Zhibing , Guo Weijie , Zeng Lei , Wu Yadi , Chen Yule , Tai Fang , Wang Yifan , Lin Yiwei , Zhang Qiang , He Yanling , Deng Jiong , Stewart Rachel L. , Wang Chi , Lin Pengnian Charles , Ghaffari Saghi , Evers B. Mark , Liu Suling , Zhou Ming-Ming , Zhou Binhua P. , Shi Jian 
Published: November 2018

AbstractBRD4 assembles transcriptional machinery at gene super-enhancer regions and governs the expression of genes that are critical for cancer progression. However, it remains unclear whether BRD4-mediated gene transcription is required for tumor cells to develop drug resistance. Our data show that prolonged treatment of luminal breast cancer cells with AKT inhibitors induces FOXO3a dephosphorylation, nuclear translocation, and disrupts its association with SirT6, eventually leading to FOXO3a acetylation as well as BRD4 recognition. Acetylated FOXO3a recognizes the BD2 domain of BRD4, recruits the BRD4/RNAPII complex to the CDK6 gene promoter, and induces its transcription. Pharmacological inhibition of either BRD4/FOXO3a association or CDK6 significantly overcomes the resistance of luminal breast cancer cells to AKT inhibitors in vitro and in vivo. Our study reports the involvement of BRD4/FOXO3a/CDK6 axis in AKTi resistance and provides potential therapeutic strategies for treating resistant breast cancer.
Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean
Authors: Becker Kevin W. , Collins James R. , Durham Bryndan P. , Groussman Ryan D. , White Angelicque E. , Fredricks Helen F. , Ossolinski Justin E. , Repeta Daniel J. , Carini Paul , Armbrust E. Virginia , Van Mooy Benjamin A. S. 
Published: November 2018

AbstractSunlight is the dominant control on phytoplankton biosynthetic activity, and darkness deprives them of their primary external energy source. Changes in the biochemical composition of phytoplankton communities over diel light cycles and attendant consequences for carbon and energy flux in environments remain poorly elucidated. Here we use lipidomic data from the North Pacific subtropical gyre to show that biosynthesis of energy-rich triacylglycerols (TAGs) by eukaryotic nanophytoplankton during the day and their subsequent consumption at night drives a large and previously uncharacterized daily carbon cycle. Diel oscillations in TAG concentration comprise 23 ± 11% of primary production by eukaryotic nanophytoplankton representing a global flux of about 2.4 Pg C yr−1. Metatranscriptomic analyses of genes required for TAG biosynthesis indicate that haptophytes and dinoflagellates are active members in TAG production. Estimates suggest that these organisms could contain as much as 40% more calories at sunset than at sunrise due to TAG production.
A downy mildew effector evades recognition by polymorphism of expression and subcellular localization
Authors: Asai Shuta , Furzer Oliver J. , Cevik Volkan , Kim Dae Sung , Ishaque Naveed , Goritschnig Sandra , Staskawicz Brian J. , Shirasu Ken , Jones Jonathan D. G. 
Published: November 2018

AbstractPathogen co-evolution with plants involves selection for evasion of host surveillance systems. The oomycete Hyaloperonospora arabidopsidis (Hpa) causes downy mildew on Arabidopsis, and race-specific interactions between Arabidopsis accessions and Hpa isolates fit the gene-for-gene model in which host resistance or susceptibility are determined by matching pairs of plant Resistance (R) genes and pathogen Avirulence (AVR) genes. Arabidopsis Col-0 carries R gene RPP4 that confers resistance to Hpa isolates Emoy2 and Emwa1, but its cognate recognized effector(s) were unknown. We report here the identification of the Emoy2 AVR effector gene recognized by RPP4 and show resistance-breaking isolates of Hpa on RPP4-containing Arabidopsis carry the alleles that either are not expressed, or show cytoplasmic instead of nuclear subcellular localization.
Plasmon induced thermoelectric effect in graphene
Authors: Shautsova Viktoryia , Sidiropoulos Themistoklis , Xiao Xiaofei , Güsken Nicholas A. , Black Nicola C. G. , Gilbertson Adam M. , Giannini Vincenzo , Maier Stefan A. , Cohen Lesley F. , Oulton Rupert F. 
Published: November 2018

AbstractGraphene has emerged as a promising material for optoelectronics due to its potential for ultrafast and broad-band photodetection. The photoresponse of graphene junctions is characterized by two competing photocurrent generation mechanisms: a conventional photovoltaic effect and a more dominant hot-carrier-assisted photothermoelectric (PTE) effect. The PTE effect is understood to rely on variations in the Seebeck coefficient through the graphene doping profile. A second PTE effect can occur across a homogeneous graphene channel in the presence of an electronic temperature gradient. Here, we study the latter effect facilitated by strongly localised plasmonic heating of graphene carriers in the presence of nanostructured electrical contacts resulting in electronic temperatures of the order of 2000 K. At certain conditions, the plasmon-induced PTE photocurrent contribution can be isolated. In this regime, the device effectively operates as a sensitive electronic thermometer and as such represents an enabling technology for development of hot carrier based plasmonic devices.
Seamless lateral graphene p–n junctions formed by selective in situ doping for high-performance photodetectors
Authors: Wang Gang , Zhang Miao , Chen Da , Guo Qinglei , Feng Xuefei , Niu Tianchao , Liu Xiaosong , Li Ang , Lai Jiawei , Sun Dong , Liao Zhimin , Wang Yongqiang , Chu Paul K. , Ding Guqiao , Xie Xiaoming , Di Zengfeng , Wang Xi 
Published: November 2018

AbstractLateral graphene p–n junctions are important since they constitute the core components in a variety of electronic/photonic systems. However, formation of lateral graphene p–n junctions with a controllable doping levels is still a great challenge due to the monolayer feature of graphene. Herein, by performing selective ion implantation and in situ growth by dynamic chemical vapor deposition, direct formation of seamless lateral graphene p–n junctions with spatial control and tunable doping is demonstrated. Uniform lattice substitution with heteroatoms is achieved in both the boron-doped and nitrogen-doped regions and photoelectrical assessment reveals that the seamless lateral p–n junctions exhibit a distinct photocurrent response under ambient conditions. As ion implantation is a standard technique in microelectronics, our study suggests a simple and effective strategy for mass production of graphene p–n junctions with batch capability and spatial controllability, which can be readily integrated into the production of graphene-based electronics and photonics.
NLRP3 lacking the leucine-rich repeat domain can be fully activated via the canonical inflammasome pathway
Authors: Hafner-Bratkovič Iva , Sušjan Petra , Lainšček Duško , Tapia-Abellán Ana , Cerović Kosta , Kadunc Lucija , Angosto-Bazarra Diego , Pelegrin Pablo , Jerala Roman 
Published: November 2018

AbstractNLRP3 is a cytosolic sensor triggered by different pathogen- and self-derived signals that plays a central role in a variety of pathological conditions, including sterile inflammation. The leucine-rich repeat domain is present in several innate immune receptors, where it is frequently responsible for sensing danger signals and regulation of activation. Here we show by reconstitution of truncated and chimeric variants intoNlrp3−/−macrophages that the leucine-rich repeat domain is dispensable for activation and self-regulation of NLRP3 by several different triggers. The pyrin domain on the other hand is required to maintain NLRP3 in the inactive conformation. A fully responsive minimal NLRP3 truncation variant reconstitutes peritonitis inNlrp3−/−mice. We demonstrate that in contrast to pathogen-activated NLRC4, the constitutively active NLRP3 molecule cannot engage wild-type NLRP3 molecules in a self-catalytic oligomerization. This lack of signal amplification is likely a protective mechanism to decrease sensitivity to endogenous triggers to impede autoinflammation.
Selective production of phase-separable product from a mixture of biomass-derived aqueous oxygenates
Authors: Wang Yehong , Peng Mi , Zhang Jian , Zhang Zhixin , An Jinghua , Du Shuyan , An Hongyu , Fan Fengtao , Liu Xi , Zhai Peng , Ma Ding , Wang Feng 
Published: November 2018

AbstractSelective conversion of an aqueous solution of mixed oxygenates produced by biomass fermentation to a value-added single product is pivotal for commercially viable biomass utilization. However, the efficiency and selectivity of the transformation remains a great challenge. Herein, we present a strategy capable of transforming ~70% of carbon in an aqueous fermentation mixture (ABE: acetone–butanol–ethanol–water) to 4-heptanone (4-HPO), catalyzed by tin-doped ceria (Sn-ceria), with a selectivity as high as 86%. Water (up to 27 wt%), detrimental to the reported catalysts for ABE conversion, was beneficial for producing 4-HPO, highlighting the feasibility of the current reaction system. In a 300 h continuous reaction over 2 wt% Sn-ceria catalyst, the average 4-HPO selectivity is maintained at 85% with 50% conversion and > 90% carbon balance. This strategy offers a route for highly efficient organic-carbon utilization, which can potentially integrate biological and chemical catalysis platforms for the robust and highly selective production of value-added chemicals.
Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs
Authors: Dufourt Jeremy , Trullo Antonio , Hunter Jennifer , Fernandez Carola , Lazaro Jorge , Dejean Matthieu , Morales Lucas , Nait-Amer Saida , Schulz Katharine N. , Harrison Melissa M. , Favard Cyril , Radulescu Ovidiu , Lagha Mounia 
Published: November 2018

AbstractPioneer transcription factors can engage nucleosomal DNA, which leads to local chromatin remodeling and to the establishment of transcriptional competence. However, the impact of enhancer priming by pioneer factors on the temporal control of gene expression and on mitotic memory remains unclear. Here we employ quantitative live imaging methods and mathematical modeling to test the effect of the pioneer factor Zelda on transcriptional dynamics and memory in Drosophila embryos. We demonstrate that increasing the number of Zelda binding sites accelerates the kinetics of nuclei transcriptional activation regardless of their transcriptional past. Despite its known pioneering activities, we show that Zelda does not remain detectably associated with mitotic chromosomes and is neither necessary nor sufficient to foster memory. We further reveal that Zelda forms sub-nuclear dynamic hubs where Zelda binding events are transient. We propose that Zelda facilitates transcriptional activation by accumulating in microenvironments where it could accelerate the duration of multiple pre-initiation steps.
Medullary bone in an Early Cretaceous enantiornithine bird and discussion regarding its identification in fossils
Authors: O’Connor Jingmai , Erickson Gregory M. , Norell Mark , Bailleul Alida M. , Hu Han , Zhou Zhonghe 
Published: November 2018

AbstractMedullary bone is an ephemeral type of bone tissue, today found only in sexually mature female birds, that provides a calcium reservoir for eggshell formation. The presence of medullary bone-like tissues in extant birds, pterosaurs, and dinosaurs distantly related to birds shows that caution must be exercised before concluding that fossils bear medullary bone. Here we describe a new specimen of pengornithid enantiornithine from the Lower Cretaceous Jiufotang Formation. Consisting of an isolated left hindlimb, the three-dimensional preservation contrasts with the crushed preservation characteristic of most Jehol specimens. Histological examinations suggest this resulted from the presence of a thick layer of highly vascular bone spanning the medullary cavities of the femur and tibiotarsus, consistent with expectations for medullary bone in extant birds. Micro-computed tomographic scans reveal small amounts of the same tissue extending into the pedal phalanges. We consider the tissue to be homologous to the medullary bone of Neornithines.
Chromatin interactions and expression quantitative trait loci reveal genetic drivers of multimorbidities
Authors: Fadason Tayaza , Schierding William , Lumley Thomas , O’Sullivan Justin M. 
Published: November 2018

AbstractClinical studies of non-communicable diseases identify multimorbidities that suggest a common set of predisposing factors. Despite the fact that humans have ~24,000 genes, we do not understand the genetic pathways that contribute to the development of multimorbid non-communicable disease. Here we create a multimorbidity atlas of traits based on pleiotropy of spatially regulated genes. Using chromatin interaction and expression Quantitative Trait Loci (eQTL) data, we analyse 20,782 variants (p < 5 × 10−6) associated with 1351 phenotypes to identify 16,248 putative spatial eQTL-eGene pairs that are involved in 76,013 short- and long-range regulatory interactions (FDR < 0.05) in different human tissues. Convex biclustering of spatial eGenes that are shared among phenotypes identifies complex interrelationships between nominally different phenotype-associated SNPs. Our approach enables the simultaneous elucidation of variant interactions with target genes that are drivers of multimorbidity, and those that contribute to unique phenotype associated characteristics.
SUMO conjugation to the pattern recognition receptor FLS2 triggers intracellular signalling in plant innate immunity
Authors: Orosa Beatriz , Yates Gary , Verma Vivek , Srivastava Anjil K. , Srivastava Moumita , Campanaro Alberto , De Vega Daniel , Fernandes Alanna , Zhang Cunjin , Lee Jack , Bennett Malcolm J. , Sadanandom Ari 
Published: November 2018

AbstractDetection of conserved microbial patterns by host cell surface pattern recognition receptors (PRRs) activates innate immunity. The FLAGELLIN-SENSITIVE 2 (FLS2) receptor perceives bacterial flagellin and recruits another PRR, BAK1 and the cytoplasmic-kinase BIK1 to form an active co-receptor complex that initiates antibacterial immunity inArabidopsis. Molecular mechanisms that transmit flagellin perception from the plasma-membrane FLS2-associated receptor complex to intracellular events are less well understood. Here, we show that flagellin induces the conjugation of the SMALL UBIQUITIN-LIKE MODIFIER (SUMO) protein to FLS2 to trigger release of BIK1. Disruption of FLS2 SUMOylation can abolish immune responses, resulting in susceptibility to bacterial pathogens inArabidopsis. We also identify the molecular machinery that regulates FLS2 SUMOylation and demonstrate a role for the deSUMOylating enzyme, Desi3a in innate immunity. Flagellin induces the degradation of Desi3a and enhances FLS2 SUMOylation to promote BIK1 dissociation and trigger intracellular immune signalling.
De novo sequencing and transcriptome assembly of Arisaema heterophyllum Blume and identification of genes involved in isoflavonoid biosynthesis
Authors: Wang Chenkai , Zhu Jinhang , Liu Miaomiao , Yang Qingshan , Wu Jiawen , Li Zegeng 
Published: November 2018

AbstractArisaema heterophyllum Blume (AhBl) is one of the valued medicinal plants. However, its genetic information is limited, which impedes further studies of this valuable resource. To investigate the genes involved in the isoflavonoid biosynthesis, we deeply performed transcriptome sequencing for AhBl. An average of 10.98 Gb clean reads were obtained based on root, tuber and leaf tissues, and 109,937 unigenes were yielded after de novo assembly. In total, 72,287 of those unigenes were annotated in at least one public database. The numbers of expressed unigenes in each tissue were 35,686, 43,363 and 47,783, respectively. The overall expression levels of transcripts in leaf were higher than those in root and tuber. Differentially expressed genes analysis indicated that a total of 12,448 shared unigenes were detected in all three tissues, 10,215 of which were higher expressed in tuber than that in root and leaf. Besides, 87 candidate unigenes that encode for enzymes involved in biosynthesis of isoflavonoid were identified and analyzed, and some key enzyme genes were experimentally validated by quantitative Real-Time PCR (qRT-PCR). This study provides a unique dataset for the systematic analysis of AhBl functional genes and expression characteristics, and facilitates the future study of the pharmacological mechanism of AhBl.
Spatiotemporal clustering of cases of Kawasaki disease and associated coronary artery aneurysms in Canada
Authors: Hearn Jason , McCrindle Brian W. , Mueller Brigitte , O’Shea Sunita , Bernknopf Bailey , Labelle Michael , Manlhiot Cedric 
Published: November 2018

AbstractDetailed epidemiologic examination of the distribution of Kawasaki disease (KD) cases could help elucidate the etiology and pathogenesis of this puzzling condition. Location of residence at KD admission was obtained for patients diagnosed in Canada (excluding Quebec) between March 2004 and March 2015. We identified 4,839 patients, 164 of whom (3.4%) developed a coronary artery aneurysm (CAA). A spatiotemporal clustering analysis was performed to determine whether non-random clusters emerged in the distributions of KD and CAA cases. A high-incidence KD cluster occurred in Toronto, ON, between October 2004 and May 2005 (116 cases; relative risk (RR) = 3.43; p < 0.001). A cluster of increased CAA frequency emerged in Mississauga, ON, between April 2004 and September 2005 (17% of KD cases; RR = 4.86). High-incidence clusters also arose in British Columbia (November 2010 to March 2011) and Alberta (January 2010 to November 2012) for KD and CAA, respectively. In an exploratory comparison between the primary KD cluster and reference groups of varying spatial and temporal origin, the main cluster demonstrated higher frequencies of conjunctivitis, oral mucosa changes and treatment with antibiotics, suggesting a possible coincident infectious process. Further spatiotemporal evaluation of KD cases might help understand the probable multifactorial etiology.