bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global pairwise RNA interaction landscapes reveal core features of protein recognition
Authors: Zhou Qin , Kunder Nikesh , De la Paz José Alberto , Lasley Alexandra E. , Bhat Vandita D. , Morcos Faruck , Campbell Zachary T. 
Published: June 2018

AbstractRNA–protein interactions permeate biology. Transcription, translation, and splicing all hinge on the recognition of structured RNA elements by RNA-binding proteins. Models of RNA–protein interactions are generally limited to short linear motifs and structures because of the vast sequence sampling required to access longer elements. Here, we develop an integrated approach that calculates global pairwise interaction scores from in vitro selection and high-throughput sequencing. We examine four RNA-binding proteins of phage, viral, and human origin. Our approach reveals regulatory motifs, discriminates between regulated and non-regulated RNAs within their native genomic context, and correctly predicts the consequence of mutational events on binding activity. We design binding elements that improve binding activity in cells and infer mutational pathways that reveal permissive versus disruptive evolutionary trajectories between regulated motifs. These coupling landscapes are broadly applicable for the discovery and characterization of protein–RNA recognition at single nucleotide resolution.
Astrometrically registered maps of H2O and SiO masers toward VX Sagittarii
Authors: Yoon Dong-Hwan , Cho Se-Hyung , Yun Youngjoo , Choi Yoon Kyung , Dodson Richard , Rioja María , Kim Jaeheon , Imai Hiroshi , Kim Dongjin , Yang Haneul , Byun Do-Young 
Published: June 2018

AbstractThe supergiant VX Sagittarii is a strong emitter of both H2O and SiO masers. However, previous VLBI observations have been performed separately, which makes it difficult to spatially trace the outward transfer of the material consecutively. Here we present the astrometrically registered, simultaneous maps of 22.2 GHz H2O and 43.1/42.8/86.2/129.3 GHz SiO masers toward VX Sagittarii. The H2O masers detected above the dust-forming layers have an asymmetric distribution. The multi-transition SiO masers are nearly circular ring, suggesting spherically symmetric wind within a few stellar radii. These results provide the clear evidence that the asymmetry in the outflow is enhanced after the smaller molecular gas clump transform into the inhomogeneous dust layers. The 129.3 GHz maser arises from the outermost region compared to that of 43.1/42.8/86.2 GHz SiO masers. The ring size of the 129.3 GHz maser is maximized around the optical maximum, suggesting that radiative pumping is dominant.
Go/No-Go task engagement enhances population representation of target stimuli in primary auditory cortex
Authors: Bagur Sophie , Averseng Martin , Elgueda Diego , David Stephen , Fritz Jonathan , Yin Pingbo , Shamma Shihab , Boubenec Yves , Ostojic Srdjan 
Published: June 2018

AbstractPrimary sensory cortices are classically considered to extract and represent stimulus features, while association and higher-order areas are thought to carry information about stimulus meaning. Here we show that this information can in fact be found in the neuronal population code of the primary auditory cortex (A1). A1 activity was recorded in awake ferrets while they either passively listened or actively discriminated stimuli in a range of Go/No-Go paradigms, with different sounds and reinforcements. Population-level dimensionality reduction techniques reveal that task engagement induces a shift in stimulus encoding from a sensory to a behaviorally driven representation that specifically enhances the target stimulus in all paradigms. This shift partly relies on task-engagement-induced changes in spontaneous activity. Altogether, we show that A1 population activity bears strong similarities to frontal cortex responses. These findings indicate that primary sensory cortices implement a crucial change in the structure of population activity to extract task-relevant information during behavior.
Dynamic strain determination using fibre-optic cables allows imaging of seismological and structural features
Authors: Jousset Philippe , Reinsch Thomas , Ryberg Trond , Blanck Hanna , Clarke Andy , Aghayev Rufat , Hersir Gylfi P. , Henninges Jan , Weber Michael , Krawczyk Charlotte M. 
Published: June 2018

AbstractNatural hazard prediction and efficient crust exploration require dense seismic observations both in time and space. Seismological techniques provide ground-motion data, whose accuracy depends on sensor characteristics and spatial distribution. Here we demonstrate that dynamic strain determination is possible with conventional fibre-optic cables deployed for telecommunication. Extending recently distributed acoustic sensing (DAS) studies, we present high resolution spatially un-aliased broadband strain data. We recorded seismic signals from natural and man-made sources with 4-m spacing along a 15-km-long fibre-optic cable layout on Reykjanes Peninsula, SW-Iceland. We identify with unprecedented resolution structural features such as normal faults and volcanic dykes in the Reykjanes Oblique Rift, allowing us to infer new dynamic fault processes. Conventional seismometer recordings, acquired simultaneously, validate the spectral amplitude DAS response between 0.1 and 100 Hz bandwidth. We suggest that the networks of fibre-optic telecommunication lines worldwide could be used as seismometers opening a new window for Earth hazard assessment and exploration.
Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta
Authors: Baron Chloé S. , Kester Lennart , Klaus Anna , Boisset Jean-Charles , Thambyrajah Roshana , Yvernogeau Laurent , Kouskoff Valérie , Lacaud Georges , van Oudenaarden Alexander , Robin Catherine 
Published: June 2018

AbstractHaematopoietic stem cells (HSCs) are generated from haemogenic endothelial (HE) cells via the formation of intra-aortic haematopoietic clusters (IAHCs) in vertebrate embryos. The molecular events controlling endothelial specification, endothelial-to-haematopoietic transition (EHT) and IAHC formation, as it occurs in vivo inside the aorta, are still poorly understood. To gain insight in these processes, we performed single-cell RNA-sequencing of non-HE cells, HE cells, cells undergoing EHT, IAHC cells, and whole IAHCs isolated from mouse embryo aortas. Our analysis identified the genes and transcription factor networks activated during the endothelial-to-haematopoietic switch and IAHC cell maturation toward an HSC fate. Our study provides an unprecedented complete resource to study in depth HSC generation in vivo. It will pave the way for improving HSC production in vitro to address the growing need for tailor-made HSCs to treat patients with blood-related disorders.
Layered liquid crystal elastomer actuators
Authors: Guin Tyler , Settle Michael J. , Kowalski Benjamin A. , Auguste Anesia D. , Beblo Richard V. , Reich Gregory W. , White Timothy J. 
Published: June 2018

AbstractLiquid crystalline elastomers (LCEs) are soft, anisotropic materials that exhibit large shape transformations when subjected to various stimuli. Here we demonstrate a facile approach to enhance the out-of-plane work capacity of these materials by an order of magnitude, to nearly 20 J/kg. The enhancement in force output is enabled by the development of a room temperature polymerizable composition used both to prepare individual films, organized via directed self-assembly to retain arrays of topological defect profiles, as well as act as an adhesive to combine the LCE layers. The material actuator is shown to displace a load >2500× heavier than its own weight nearly 0.5 mm.
Coherent two-dimensional electronic mass spectrometry
Authors: Roeding Sebastian , Brixner Tobias 
Published: June 2018

AbstractCoherent two-dimensional (2D) optical spectroscopy has revolutionized our ability to probe many types of couplings and ultrafast dynamics in complex quantum systems. The dynamics and function of any quantum system strongly depend on couplings to the environment. Thus, studying coherent interactions for different environments remains a topic of tremendous interest. Here we introduce coherent 2D electronic mass spectrometry that allows 2D measurements on effusive molecular beams and thus on quantum systems with minimum system–bath interaction and employ this to identify the major ionization pathway of 3d Rydberg states in NO2. Furthermore, we present 2D spectra of multiphoton ionization, disclosing distinct differences in the nonlinear response functions leading to the ionization products. We also realize the equivalent of spectrally resolved transient-absorption measurements without the necessity for acquiring weak absorption changes. Using time-of-flight detection introduces cations as an observable, enabling the 2D spectroscopic study on isolated systems of photophysical and photochemical reactions.
Direct evidence for hula twist and single-bond rotation photoproducts
Authors: Gerwien Aaron , Schildhauer Monika , Thumser Stefan , Mayer Peter , Dube Henry 
Published: June 2018

AbstractPhotoisomerization reactions are quintessential processes driving molecular machines and motors, govern smart materials, catalytic processes, and photopharmacology, and lie at the heart of vision, phototaxis, or vitamin production. Despite this plethora of applications fundamental photoisomerization mechanisms are not well understood at present. The famous hula-twist motion—a coupled single and double-bond rotation—was proposed to explain proficient photoswitching in restricted environments but fast thermal follow-up reactions hamper identification of primary photo products. Herein we describe an asymmetric chromophore possessing four geometrically distinct diastereomeric states that do not interconvert thermally and can be crystallized separately. Employing this molecular setup direct and unequivocal evidence for the hula-twist photoreaction and for photoinduced single-bond rotation is obtained. The influences of the surrounding medium and temperature are quantified and used to favor unusual photoreactions. Based on our findings molecular engineers will be able to implement photo control of complex molecular motions more consciously.
Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks
Authors: Choy Mun-Kit , Javierre Biola M. , Williams Simon G. , Baross Stephanie L. , Liu Yingjuan , Wingett Steven W. , Akbarov Artur , Wallace Chris , Freire-Pritchett Paula , Rugg-Gunn Peter J. , Spivakov Mikhail , Fraser Peter , Keavney Bernard D. 
Published: June 2018

AbstractLong-range chromosomal interactions bring distal regulatory elements and promoters together to regulate gene expression in biological processes. By performing promoter capture Hi-C (PCHi-C) on human embryonic stem cell-derived cardiomyocytes (hESC-CMs), we show that such promoter interactions are a key mechanism by which enhancers contact their target genes after hESC-CM differentiation from hESCs. We also show that the promoter interactome of hESC-CMs is associated with expression quantitative trait loci (eQTLs) in cardiac left ventricular tissue; captures the dynamic process of genome reorganisation after hESC-CM differentiation; overlaps genome-wide association study (GWAS) regions associated with heart rate; and identifies new candidate genes in such regions. These findings indicate that regulatory elements in hESC-CMs identified by our approach control gene expression involved in ventricular conduction and rhythm of the heart. The study of promoter interactions in other hESC-derived cell types may be of utility in functional investigation of GWAS-associated regions.
Zero-static power radio-frequency switches based on MoS2 atomristors
Authors: Kim Myungsoo , Ge Ruijing , Wu Xiaohan , Lan Xing , Tice Jesse , Lee Jack C. , Akinwande Deji 
Published: June 2018

AbstractRecently, non-volatile resistance switching or memristor (equivalently, atomristor in atomic layers) effect was discovered in transitional metal dichalcogenides (TMD) vertical devices. Owing to the monolayer-thin transport and high crystalline quality, ON-state resistances below 10 Ω are achievable, making MoS2 atomristors suitable as energy-efficient radio-frequency (RF) switches. MoS2 RF switches afford zero-hold voltage, hence, zero-static power dissipation, overcoming the limitation of transistor and mechanical switches. Furthermore, MoS2 switches are fully electronic and can be integrated on arbitrary substrates unlike phase-change RF switches. High-frequency results reveal that a key figure of merit, the cutoff frequency (fc), is about 10 THz for sub-μm2 switches with favorable scaling that can afford fc above 100 THz for nanoscale devices, exceeding the performance of contemporary switches that suffer from an area-invariant scaling. These results indicate a new electronic application of TMDs as non-volatile switches for communication platforms, including mobile systems, low-power internet-of-things, and THz beam steering.
Natural selection of a GSK3 determines rice mesocotyl domestication by coordinating strigolactone and brassinosteroid signaling
Authors: Sun Shiyong , Wang Tao , Wang Linlin , Li Xiaoming , Jia Yancui , Liu Chang , Huang Xuehui , Xie Weibo , Wang Xuelu 
Published: June 2018

AbstractMesocotyl is the crucial organ for pushing buds out of deep water or soil after germination in monocots. Deep direct seeding or mechanized dry seeding cultivation practice requires rice cultivars having long mesocotyl. However, the mechanisms of mesocotyl elongation and domestication remain unknown. Here, our genome-wide association study (GWAS) reveals that natural variations of OsGSK2, a conserved GSK3-like kinase involved in brassinosteroid signaling, determine rice mesocotyl length variation. Variations in the coding region of OsGSK2 alter its kinase activity. It is selected for mesocotyl length variation during domestication. Molecular analyses show that brassinosteroid-promoted mesocotyl elongation functions by suppressing the phosphorylation of an U-type cyclin, CYC U2, by OsGSK2. Importantly, the F-box protein D3, a major positive component in strigolactone signaling, can degrade the OsGSK2-phosphorylated CYC U2 to inhibit mesocotyl elongation. Together, these results suggest that OsGSK2 is selected to regulate mesocotyl length by coordinating strigolactone and brassinosteroid signaling during domestication.
Very large tunneling magnetoresistance in layered magnetic semiconductor CrI3
Authors: Wang Zhe , Gutiérrez-Lezama Ignacio , Ubrig Nicolas , Kroner Martin , Gibertini Marco , Taniguchi Takashi , Watanabe Kenji , Imamoğlu Ataç , Giannini Enrico , Morpurgo Alberto F. 
Published: June 2018

AbstractMagnetic layered van der Waals crystals are an emerging class of materials giving access to new physical phenomena, as illustrated by the recent observation of 2D ferromagnetism in Cr2Ge2Te6 and CrI3. Of particular interest in semiconductors is the interplay between magnetism and transport, which has remained unexplored. Here we report magneto-transport measurements on exfoliated CrI3 crystals. We find that tunneling conduction in the direction perpendicular to the crystalline planes exhibits a magnetoresistance as large as 10,000%. The evolution of the magnetoresistance with magnetic field and temperature reveals that the phenomenon originates from multiple transitions to different magnetic states, whose possible microscopic nature is discussed on the basis of all existing experimental observations. This observed dependence of the conductance of a tunnel barrier on its magnetic state is a phenomenon that demonstrates the presence of a strong coupling between transport and magnetism in magnetic van der Waals semiconductors.
Prolonged abstinence from cocaine or morphine disrupts separable valuations during decision conflict
Authors: Sweis Brian M. , Redish A. David , Thomas Mark J. 
Published: June 2018

AbstractNeuroeconomic theories propose changes in decision making drive relapse in recovering drug addicts, resulting in continued drug use despite stated wishes not to. Such conflict is thought to arise from multiple valuation systems dependent on separable neural components, yet many neurobiology of addiction studies employ only simple tests of value. Here, we tested in mice how prolonged abstinence from different drugs affects behavior in a neuroeconomic foraging task that reveals multiple tests of value. Abstinence from repeated cocaine and morphine disrupts separable decision-making processes. Cocaine alters deliberation-like behavior prior to choosing a preferred though economically unfavorable offer, while morphine disrupts re-evaluations after rapid initial decisions. These findings suggest that different drugs have long-lasting effects precipitating distinct decision-making vulnerabilities. Our approach can guide future refinement of decision-making behavioral paradigms and highlights how grossly similar behavioral maladaptations may mask multiple underlying, parallel, and dissociable processes that treatments for addiction could potentially target.
Lacrimal Canaliculus Imaging Using Optical Coherence Tomography Dacryography
Authors: Fujimoto Masahiro , Uji Akihito , Ogino Ken , Akagi Tadamichi , Yoshimura Nagahisa 
Published: June 2018

AbstractLacrimal canaliculus (LC) has a key role in tear drainage, but it is difficult to evaluate the LC in detail, using the existing examinations. In this study, our novel LC imaging technique provided the high-resolution images of LC in a non-invasive manner. Three-dimensional images of LC were acquired via the palpebral conjunctiva from 20 healthy volunteers (20 eyes) and 10 patients with various lacrimal disorders (10 eyes), using optical coherence tomography (OCT) dacryography (OCTD). The LC images showed morphological differences between the vertical and horizontal segments. The function of LC could be evaluated by measuring the intralumen signal intensity over time after instillation of a contrast agent (2% rebamipide ophthalmic suspension). OCTD clearly visualised the blind extremity of the LC in four patients with punctal obstruction, which was useful for deciding the punctal incision location. In one patient with canalicular obstruction, contrast agent successfully highlighted the LC that had become narrow toward the site of obstruction. Significant differences were not found in the function and morphology of LC between the patients with NLDO and the healthy subjects. OCTD may be a useful tool for LC imaging, because it facilitates quantitative and simultaneous evaluation of LC morphology and function.
Evaluating the Contribution of North American Zoos and Aquariums to Endangered Species Recovery
Authors: Che-Castaldo Judy P. , Grow Shelly A. , Faust Lisa J. 
Published: June 2018

AbstractThe challenge of recovering threatened species necessitates collaboration among diverse conservation partners. Zoos and aquariums have long partnered with other conservation organizations and government agencies to help recover species through a range ofin situandex situconservation projects. These efforts tend to be conducted by individual facilities and for individual species, and thus the scope and magnitude of these actions at the national level are not well understood. Here we evaluate the means and extent to which North American zoos and aquariums contribute to the recovery of species listed under the U.S. Endangered Species Act (ESA), by synthesizing data from federal recovery plans for listed species and from annual surveys conducted by the Association of Zoos and Aquariums. We found that in addition to managingex situassurance populations, zoos frequently conduct conservation research and field-based population monitoring and assessments. Cooperatively managed populations in zoos tend to focus on species that are not listed on the ESA or on foreign listings, and thus it may be beneficial for zoos to manage more native threatened species. Our results highlight the existing contributions, but also identify additional opportunities for the zoo community to help recover threatened species.
Motion cues tune social influence in shoaling fish
Authors: Lemasson Bertrand , Tanner Colby , Woodley Christa , Threadgill Tammy , Qarqish Shea , Smith David 
Published: June 2018

AbstractSocial interactions have important consequences for individual fitness. Collective actions, however, are notoriously context-dependent and identifying how animals rapidly weigh the actions of others despite environmental uncertainty remains a fundamental challenge in biology. By exposing zebrafish (Danio rerio) to virtual fish silhouettes in a maze we isolated how the relative strength of a visual feature guides individual directional decisions and, subsequently, tunes social influence. We varied the relative speed and coherency with which a portion of silhouettes adopted a direction (leader/distractor ratio) and established that solitary zebrafish display a robust optomotor response to follow leader silhouettes that moved much faster than their distractors, regardless of stimulus coherency. Although recruitment time decreased as a power law of zebrafish group size, individual decision times retained a speed-accuracy trade-off, suggesting a benefit to smaller group sizes in collective decision-making. Directional accuracy improved regardless of group size in the presence of the faster moving leader silhouettes, but without these stimuli zebrafish directional decisions followed a democratic majority rule. Our results show that a large difference in movement speeds can guide directional decisions within groups, thereby providing individuals with a rapid and adaptive means of evaluating social information in the face of uncertainty.
Live cell imaging reveals focal adhesions mechanoresponses in mammary epithelial cells under sustained equibiaxial stress
Authors: Sigaut Lorena , von Bilderling Catalina , Bianchi Micaela , Burdisso Juan Eduardo , Gastaldi Laura , Pietrasanta Lía Isabel 
Published: June 2018

AbstractMechanical stimuli play a key role in many cell functions such as proliferation, differentiation and migration. In the mammary gland, mechanical signals such as the distension of mammary epithelial cells due to udder filling are proposed to be directly involved during lactation and involution. However, the evolution of focal adhesions -specialized multiprotein complexes that mechanically connect cells with the extracellular matrix- during the mammary gland development, as well as the influence of the mechanical stimuli involved, remains unclear. Here we present the use of an equibiaxial stretching device for exerting a sustained normal strain to mammary epithelial cells while quantitatively assessing cell responses by fluorescence imaging techniques. Using this approach, we explored changes in focal adhesion dynamics in HC11 mammary cells in response to a mechanical sustained stress, which resembles the physiological stimuli. We studied the relationship between a global stress and focal adhesion assembly/disassembly, observing an enhanced persistency of focal adhesions under strain as well as an increase in their size. At a molecular level, we evaluated the mechanoresponses of vinculin and zyxin, two focal adhesion proteins postulated as mechanosensors, observing an increment in vinculin molecular tension and a slower zyxin dynamics while increasing the applied normal strain.