bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geomorphic Evolution of a Gravel‐Bed River Under Sediment‐Starved Versus Sediment‐Rich Conditions: River Response to the World's Largest Dam Removal
Authors: East A. E. , Logan J. B. , Mastin M. C. , Ritchie A. C. , Bountry J. A. , Magirl C. S. , Sankey J. B. 
Published: December 2018

AbstractUnderstanding river response to sediment pulses is a fundamental problem in geomorphic process studies, with myriad implications for river management. However, because large sediment pulses are rare and usually unanticipated, they are seldom studied at field scale. We examine fluvial response to a massive (~20 Mt) sediment pulse released by the largest dam removal globally, on the Elwha River, Washington, United States, in an 11‐year before‐after/control‐impact study of channel morphology and grain size. We test the hypothesis that for a given flow magnitude, greater geomorphic change occurs under sediment‐rich conditions than under sediment‐starved conditions. Channel response to flow forcing was significantly different during the sediment‐pulse peak, 1–2 years after dam removal began, than earlier or later. During peak sediment supply our hypothesis was supported; major geomorphic change occurred under low flows and unit stream power ≤60 W/m2. However, by 4–6 years after dam removal began, rates of geomorphic change and sensitivity to stream power had decreased substantially such that our hypothesis was no longer unequivocally supported. These findings are consistent with a two‐phase conceptual model of dam‐removal response, involving a transport‐limited state followed by a more supply‐limited state. From comparisons with other dam removals and natural sediment pulses, we infer that the longevity of sediment‐pulse signals in gravel‐bed rivers depends upon gradient, river discharge, valley morphology, and sediment grain size. Stream power associated with substantial geomorphic change varies with sediment supply, such that assigning a general threshold stream power to gravel‐bed rivers may be untenable.
Resistance Is Not Futile: Grain Resistance Controls on Observed Critical Shields Stress Variations
Authors: Yager Elowyn M. , Schmeeckle Mark W. , Badoux Alexandre 
Published: December 2018

AbstractEstimates of the onset of sediment motion are integral for flood protection and river management but are often highly inaccurate. The critical shear stress (τ*c) for grain entrainment is often assumed constant, but measured values can vary by almost an order of magnitude between rivers. Such variations are typically explained by differences in measurement methodology, grain size distributions, or flow hydraulics, whereas grain resistance to motion is largely assumed to be constant. We demonstrate that grain resistance varies strongly with the bed structure, which is encapsulated by the particle height above surrounding sediment (protrusion, p) and intergranular friction (ϕf). We incorporate these parameters into a novel theory that correctly predicts resisting forces estimated in the laboratory, field, and a numerical model. Our theory challenges existing models, which significantly overestimate bed mobility. In our theory, small changes in p and ϕf can induce large changes in τ*c without needing to invoke variations in measurement methods or grain size. A data compilation also reveals that scatter in empirical values of τ*c can be partly explained by differences in p between rivers. Therefore, spatial and temporal variations in bed structure can partly explain the deviation of τ*c from an assumed constant value. Given that bed structure is known to vary with applied shear stresses and upstream sediment supply, we conclude that a constant τ*c is unlikely. Values of τ*c are not interchangeable between streams, or even through time in a given stream, because they are encoded with the channel history.
Occurrence and Origin of Methane Entrapped in Sediments and Rocks of a Calcareous, Alpine Glacial Catchment
Authors: Zhu Biqing , Henneberger Ruth , Weissert Helmut , Zeyer Josef , Schroth Martin H. 
Published: December 2018

AbstractGlacial ecosystems are an important indicator of climate change, and dynamics of the greenhouse gas methane (CH4) in these systems has become a major research topic of late. We investigated occurrence and origin of recently discovered, sediment‐entrapped CH4 within the Wildstrubel glacial catchment (Switzerland) using geochemical analyses on gas extracted from sediments and rocks, including gas content and CH4 stable isotope measurements, and computation of gas wetness (ratio of CH4 to ethane and propane). We also examined the potential occurrence of microbial CH4 production in subglacial, supraglacial, and glacier forefield sediments based on molecular analyses targeting mcrA (a marker gene for microbial CH4 production) and based on observed CH4 production during laboratory incubation experiments. Substantial amounts of entrapped CH4 were detected in all sediment (65.7 ± 28.6 μg CH4/g) and most rock samples (up to 145.5 μg CH4/g). Similar gas wetness (0.7–126.7) and CH4 stable isotope values (δ13CCH4: −26.9‰ to −31.2‰, δDCH4: −118.5‰ to −158.6‰) in sediment and rock samples provided strong evidence that entrapped CH4 was of common, thermogenic origin. Molecular analyses (up to ~105 mcrA gene copies per gram) and laboratory incubation experiments (production rates up to 1.55 μg CH4 g−1 day−1) provided evidence for local hot spots of viable methanogens in waterlogged, glacier forefield sediments but not in subglacial sediments. Nonetheless, microbial CH4 production appeared to be only of minor importance at our field site, as indicated by results of our geochemical analyses. Our findings illustrate the crucial importance of appropriate geochemical analyses to provide solid evidence on the origin of CH4 in glacial systems.
Observation of Short‐Period Ionospheric Disturbances Using a Portable Digital Ionosonde at Sanya
Authors: Lan Jiaping , Ning Baiqi , Li Guozhu , Zhu Zhengping , Hu Lianhuan , Sun Wenjie 
Published: December 2018

AbstractA number of ionosondes have been operated in China to detect ionospheric disturbances for many years. These ionosondes, however, are not very suitable for the short‐period (<15 min) disturbances due to their poor time resolutions (>5 min). During recent years, the Institute of Geology and Geophysics, Chinese Academy of Sciences, together with the South Central University for Nationalities has been developing a portable digital ionosonde (PDI) equipped with the capability to detect and characterize small‐scale/short‐period ionospheric disturbances and to be quickly assembled and set up at temporary field stations for low‐latitude campaign coordinated observations. The PDI uses a set of technologies (e.g., code multiplexing and antenna/transmitter matching) that allow it to obtain quality Doppler ionograms at a good time resolution with small transmitting antennas. A preliminary analysis of observations by the PDI at Sanya (18.3°N, 109.6°E) shows the presence of ionospheric disturbances with periods ranging between several and tens of minutes. Interestingly, the disturbances (with different periods) were found to simultaneously occur at different F region altitudes, for example, with periods of ~5 and 20 min below and above ~180 km, respectively. The absence of shorter‐period disturbance at higher altitude is consistent with acoustic gravity waves through the region with intrinsic periods above the Brunt‐Väisälä period. The short‐period disturbances observed in F region bottomside are not evident in total electron content. The results demonstrate the capability of PDI to detect ionospheric disturbances with temporal scales down to a few minutes in routine ionogram mode. Future prospects of PDI are outlined.
Whole genome MBD-seq and RRBS analyses reveal that hypermethylation of gastrointestinal hormone receptors is associated with gastric carcinogenesis
Authors: Kim Hee-Jin , Kang Tae-Wook , Haam Keeok , Kim Mirang , Kim Seon-Kyu , Kim Seon-Young , Lee Sang-Il , Song Kyu-Sang , Jeong Hyun-Yong , Kim Yong Sung 
Published: December 2018

AbstractDNA methylation is a regulatory mechanism in epigenetics that is frequently altered during human carcinogenesis. To detect critical methylation events associated with gastric cancer (GC), we compared three DNA methylomes from gastric mucosa (GM), intestinal metaplasia (IM), and gastric tumor (GT) cells that were microscopically dissected from an intestinal-type early gastric cancer (EGC) using methylated DNA binding domain sequencing (MBD-seq) and reduced representation bisulfite sequencing (RRBS) analysis. In this study, we focused on differentially methylated promoters (DMPs) that could be directly associated with gene expression. We detected 2,761 and 677 DMPs between the GT and GM by MBD-seq and RRBS, respectively, and for a total of 3,035 DMPs. Then, 514 (17%) of all DMPs were detected in the IM genome, which is a precancer of GC, supporting that some DMPs might represent an early event in gastric carcinogenesis. A pathway analysis of all DMPs demonstrated that 59 G protein-coupled receptor (GPCR) genes linked to the hypermethylated DMPs were significantly enriched in a neuroactive ligand–receptor interaction pathway. Furthermore, among the 59 GPCRs, six GI hormone receptor genes (NPY1R, PPYR1, PTGDR, PTGER2, PTGER3, and SSTR2) that play an inhibitory role in the secretion of gastrin or gastric acid were selected and validated as potential biomarkers for the diagnosis or prognosis of GC patients in two cohorts. These data suggest that the loss of function of gastrointestinal (GI) hormone receptors by promoter methylation may lead to gastric carcinogenesis because gastrin and gastric acid have been known to play a role in cell differentiation and carcinogenesis in the GI tract.
Neuronal photoactivation through second-harmonic near-infrared absorption by gold nanoparticles
Authors: de Boer Wieteke D. A. M. , Hirtz Jan J. , Capretti Antonio , Gregorkiewicz Tom , Izquierdo-Serra Mercè , Han Shuting , Dupre Christophe , Shymkiv Yuriy , Yuste Rafael 
Published: December 2018

AbstractOptical activation of neurons requires genetic manipulation or the use of chemical photoactivators with undesirable side effects. As a solution to these disadvantages, here, we demonstrate optically evoked neuronal activity in mouse cortical neurons in acute slices and in vivo by nonlinear excitation of gold nanoparticles. In addition, we use this approach to stimulate individual epitheliomuscular cells and evoke body contractions in Hydra vulgaris. To achieve this, we use a low-power pulsed near-infrared excitation at the double-wavelength of the plasmon resonance of gold nanoparticles, which enables optical sectioning and allows for high spatial precision and large penetration depth. The effect is explained by second-harmonic Mie scattering, demonstrating light absorption by a second-order nonlinear process, which enables photothermal stimulation of the cells. Our approach also minimizes photodamage, demonstrating a major advancement towards precise and harmless photoactivation for neuroscience and human therapeutics.
Sharpening emitter localization in front of a tuned mirror
Authors: Heil Hannah S. , Schreiber Benjamin , Götz Ralph , Emmerling Monika , Dabauvalle Marie-Christine , Krohne Georg , Höfling Sven , Kamp Martin , Sauer Markus , Heinze Katrin G. 
Published: December 2018

AbstractSingle-molecule localization microscopy (SMLM) aims for maximized precision and a high signal-to-noise ratio1. Both features can be provided by placing the emitter in front of a metal-dielectric nanocoating that acts as a tuned mirror2–4. Here, we demonstrate that a higher photon yield at a lower background on biocompatible metal-dielectric nanocoatings substantially improves SMLM performance and increases the localization precision by up to a factor of two. The resolution improvement relies solely on easy-to-fabricate nanocoatings on standard glass coverslips and is spectrally and spatially tunable by the layer design and wavelength, as experimentally demonstrated for dual-color SMLM in cells.
Magnetic field sensors using arrays of electrospun magnetoelectric Janus nanowires
Authors: Bauer Matthew J. , Wen Xiao , Tiwari Prabal , Arnold David P. , Andrew Jennifer S. 
Published: December 2018

AbstractThe fabrication and characterization of the first magnetoelectric sensors utilizing arrays of Janus magnetoelectric composite nanowires composed of barium titanate and cobalt ferrite are presented. By utilizing magnetoelectric nanowires suspended across electrodes above the substrate, substrate clamping is reduced when compared to layered thin-film architectures; this results in enhanced magnetoelectric coupling. Janus magnetoelectric nanowires are fabricated by sol–gel electrospinning, and their length is controlled through the electrospinning and calcination conditions. Using a directed nanomanufacturing approach, the nanowires are then assembled onto pre-patterned metal electrodes on a silicon substrate using dielectrophoresis. Using this process, functional magnetic field sensors are formed by connecting many nanowires in parallel. The observed magnetic field sensitivity from the parallel array of nanowires is 0.514 ± .027 mV Oe−1 at 1 kHz, which translates to a magnetoelectric coefficient of 514 ± 27 mV cm−1 Oe−1.
Integrative system biology analyses of CRISPR-edited iPSC-derived neurons and human brains reveal deficiencies of presynaptic signaling in FTLD and PSP
Authors: Jiang Shan , Wen Natalie , Li Zeran , Dube Umber , Del Aguila Jorge , Budde John , Martinez Rita , Hsu Simon , Fernandez Maria V. , Cairns Nigel J. ,   Dominantly Inherited Alzheimer Network (DIAN),   International FTD-Genomics Consortium (IFGC), Harari Oscar , Cruchaga Carlos , Karch Celeste M. 
Published: December 2018

AbstractMutations in the microtubule-associated protein tau (MAPT) gene cause autosomal dominant frontotemporal lobar degeneration with tau inclusions (FTLD-tau).MAPTp.R406W carriers present clinically with progressive memory loss and neuropathologically with neuronal and glial tauopathy. However, the pathogenic events triggered by the expression of the mutant tau protein remain poorly understood. To identify the genes and pathways that are dysregulated in FTLD-tau, we performed transcriptomic analyses in induced pluripotent stem cell (iPSC)–derived neurons carryingMAPTp.R406W and CRISPR/Cas9-corrected isogenic controls. We found that the expression of theMAPTp.R406W mutation was sufficient to create a significantly different transcriptomic profile compared with that of the isogeneic controls and to cause the differential expression of 328 genes. Sixty-one of these genes were also differentially expressed in the same direction betweenMAPTp.R406W carriers and pathology-free human control brains. We found that genes differentially expressed in the stem cell models and human brains were enriched for pathways involving gamma-aminobutyric acid (GABA) receptors and pre-synaptic function. The expression of GABA receptor genes, includingGABRB2andGABRG2, were consistently reduced in iPSC-derived neurons and brains fromMAPTp.R406W carriers. Interestingly, we found that GABA receptor genes, includingGABRB2andGABRG2, are significantly lower in symptomatic mouse models of tauopathy, as well as in brains with progressive supranuclear palsy. Genome wide association analyses reveal that common variants withinGABRB2are associated with increased risk for frontotemporal dementia (P < 1 × 10−3). Thus, our systems biology approach, which leverages molecular data from stem cells, animal models, and human brain tissue can reveal novel disease mechanisms. Here, we demonstrate thatMAPTp.R406W is sufficient to induce changes in GABA-mediated signaling and synaptic function, which may contribute to the pathogenesis of FTLD-tau and other primary tauopathies.
Cyclin A2/E1 activation defines a hepatocellular carcinoma subclass with a rearrangement signature of replication stress
Authors: Bayard Quentin , Meunier Léa , Peneau Camille , Renault Victor , Shinde Jayendra , Nault Jean-Charles , Mami Iadh , Couchy Gabrielle , Amaddeo Giuliana , Tubacher Emmanuel , Bacq Delphine , Meyer Vincent , La Bella Tiziana , Debaillon-Vesque Audrey , Bioulac-Sage Paulette , Seror Olivier , Blanc Jean-Frédéric , Calderaro Julien , Deleuze Jean-François , Imbeaud Sandrine , Zucman-Rossi Jessica , Letouzé Eric 
Published: December 2018

AbstractCyclins A2 and E1 regulate the cell cycle by promoting S phase entry and progression. Here, we identify a hepatocellular carcinoma (HCC) subgroup exhibiting cyclin activation through various mechanisms including hepatitis B virus (HBV) and adeno-associated virus type 2 (AAV2) insertions, enhancer hijacking and recurrent CCNA2 fusions. Cyclin A2 or E1 alterations define a homogenous entity of aggressive HCC, mostly developed in non-cirrhotic patients, characterized by a transcriptional activation of E2F and ATR pathways and a high frequency of RB1 and PTEN inactivation. Cyclin-driven HCC display a unique signature of structural rearrangements with hundreds of tandem duplications and templated insertions frequently activating TERT promoter. These rearrangements, strongly enriched in early-replicated active chromatin regions, are consistent with a break-induced replication mechanism. Pan-cancer analysis reveals a similar signature in BRCA1-mutated breast and ovarian cancers. Together, this analysis reveals a new poor prognosis HCC entity and a rearrangement signature related to replication stress.
Neural representation of visual concepts in people born blind
Authors: Striem-Amit Ella , Wang Xiaoying , Bi Yanchao , Caramazza Alfonso 
Published: December 2018

AbstractHow do we represent information without sensory features? How are abstract concepts like “freedom”, devoid of external perceptible referents, represented in the brain? Here, to address the role of sensory information in the neural representation of concepts, we used fMRI to investigate how people born blind process concepts whose referents are imperceptible to them because of their visual nature (“rainbow”, “red”). Activity for these concepts was compared to that of sensorially-perceptible referents (“rain”), classical abstract concepts (“justice”) and concrete concepts (“cup”), providing a gradient between fully concrete and fully abstract concepts in the blind. We find that anterior temporal lobe (ATL) responses track concept perceptibility and objecthood: preference for imperceptible object concepts was found in dorsal ATL, for abstract (non-object, non-referential) concepts in lateral ATL, and for perceptible concepts in medial ATL. These findings point to a new division-of-labor among aspects of ATL in representing conceptual properties that are abstract in different ways.
Frequency-tunable toughening in a polymer-metal-ceramic stack using an interfacial molecular nanolayer
Authors: Kwan Matthew , Braccini Muriel , Lane Michael W. , Ramanath Ganpati 
Published: December 2018

AbstractInterfacial toughening in composite materials is reasonably well understood for static loading, but little is known for cyclic loading. Here, we demonstrate that introducing an interfacial molecular nanolayer at the metal-ceramic interface of a layered polymer-metal-ceramic stack triples the fracture energy for ~75–300 Hz loading, yielding 40% higher values than the static-loading fracture energy. We show that this unexpected frequency-dependent toughening is underpinned by nanolayer-induced interface strengthening, which facilitates load transfer to, and plasticity in, the polymer layer. Above a threshold interfacial bond strength, the toughening magnitude and frequency range are primarily controlled by the frequency- and temperature-dependent rheological properties of the polymer. These results indicate the tunability of the toughening behavior through suitable choice of interfacial molecular layers and polymers. Our findings open up possibilities for realizing novel composites with inorganic-organic interfaces, e.g., arresting crack growth or stimulating controlled fracture triggered by loads with specific frequency characteristics.
Decoding arm speed during reaching
Authors: Inoue Yoh , Mao Hongwei , Suway Steven B. , Orellana Josue , Schwartz Andrew B. 
Published: December 2018

AbstractNeural prostheses decode intention from cortical activity to restore upper extremity movement. Typical decoding algorithms extract velocity—a vector quantity with direction and magnitude (speed) —from neuronal firing rates. Standard decoding algorithms accurately recover arm direction, but the extraction of speed has proven more difficult. We show that this difficulty is due to the way speed is encoded by individual neurons and demonstrate how standard encoding-decoding procedures produce characteristic errors. These problems are addressed using alternative brain–computer interface (BCI) algorithms that accommodate nonlinear encoding of speed and direction. Our BCI approach leads to skillful control of both direction and speed as demonstrated by stereotypic bell-shaped speed profiles, straight trajectories, and steady cursor positions before and after the movement.
Pan-cancer characterisation of microRNA across cancer hallmarks reveals microRNA-mediated downregulation of tumour suppressors
Authors: Dhawan Andrew , Scott Jacob G. , Harris Adrian L. , Buffa Francesca M. 
Published: December 2018

AbstractmicroRNAs are key regulators of the human transcriptome across a number of diverse biological processes, such as development, aging and cancer, where particular miRNAs have been identified as tumour suppressive and oncogenic. In this work, we elucidate, in a comprehensive manner, across 15 epithelial cancer types comprising 7316 clinical samples from the Cancer Genome Atlas, the association of miRNA expression and target regulation with the phenotypic hallmarks of cancer. Utilising penalised regression techniques to integrate transcriptomic, methylation and mutation data, we find evidence for a complex map of interactions underlying the relationship of miRNA regulation and the hallmarks of cancer. This highlighted high redundancy for the oncomiR-1 cluster of oncogenic miRNAs, in particular hsa-miR-17-5p. In addition, we reveal extensive miRNA regulation of tumour suppressor genes such as PTEN, FAT4 and CDK12, uncovering an alternative mechanism of repression in the absence of mutation, methylation or copy number changes.
Role of NS1 antibodies in the pathogenesis of acute secondary dengue infection
Authors: Jayathilaka Deshni , Gomes Laksiri , Jeewandara Chandima , Jayarathna Geethal. S. Bandara , Herath Dhanushka , Perera Pathum Asela , Fernando Samitha , Wijewickrama Ananda , Hardman Clare S. , Ogg Graham S. , Malavige Gathsaurie Neelika 
Published: December 2018

AbstractThe role of NS1-specific antibodies in the pathogenesis of dengue virus infection is poorly understood. Here we investigate the immunoglobulin responses of patients with dengue fever (DF) and dengue hemorrhagic fever (DHF) to NS1. Antibody responses to recombinant-NS1 are assessed in serum samples throughout illness of patients with acute secondary DENV1 and DENV2 infection by ELISA. NS1 antibody titres are significantly higher in patients with DHF compared to those with DF for both serotypes, during the critical phase of illness. Furthermore, during both acute secondary DENV1 and DENV2 infection, the antibody repertoire of DF and DHF patients is directed towards distinct regions of the NS1 protein. In addition, healthy individuals, with past non-severe dengue infection have a similar antibody repertoire as those with mild acute infection (DF). Therefore, antibodies that target specific NS1 epitopes could predict disease severity and be of potential benefit in aiding vaccine and treatment design.