bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generic decoding of seen and imagined objects using hierarchical visual features
Authors: Horikawa Tomoyasu , Kamitani Yukiyasu 
Published: May 2017

AbstractObject recognition is a key function in both human and machine vision. While brain decoding of seen and imagined objects has been achieved, the prediction is limited to training examples. We present a decoding approach for arbitrary objects using the machine vision principle that an object category is represented by a set of features rendered invariant through hierarchical processing. We show that visual features, including those derived from a deep convolutional neural network, can be predicted from fMRI patterns, and that greater accuracy is achieved for low-/high-level features with lower-/higher-level visual areas, respectively. Predicted features are used to identify seen/imagined object categories (extending beyond decoder training) from a set of computed features for numerous object images. Furthermore, decoding of imagined objects reveals progressive recruitment of higher-to-lower visual representations. Our results demonstrate a homology between human and machine vision and its utility for brain-based information retrieval.
Deterministic strain-induced arrays of quantum emitters in a two-dimensional semiconductor
Authors: Branny Artur , Kumar Santosh , Proux Raphaël , Gerardot Brian D 
Published: May 2017

AbstractAn outstanding challenge in quantum photonics is scalability, which requires positioning of single quantum emitters in a deterministic fashion. Site positioning progress has been made in established platforms including defects in diamond and self-assembled quantum dots, albeit often with compromised coherence and optical quality. The emergence of single quantum emitters in layered transition metal dichalcogenide semiconductors offers new opportunities to construct a scalable quantum architecture. Here, using nanoscale strain engineering, we deterministically achieve a two-dimensional lattice of quantum emitters in an atomically thin semiconductor. We create point-like strain perturbations in mono- and bi-layer WSe2 which locally modify the band-gap, leading to efficient funnelling of excitons towards isolated strain-tuned quantum emitters that exhibit high-purity single photon emission. We achieve near unity emitter creation probability and a mean positioning accuracy of 120±32 nm, which may be improved with further optimization of the nanopillar dimensions.
Large-scale quantum-emitter arrays in atomically thin semiconductors
Authors: Palacios-Berraquero Carmen , Kara Dhiren M. , Montblanch Alejandro R.-P. , Barbone Matteo , Latawiec Pawel , Yoon Duhee , Ott Anna K. , Loncar Marko , Ferrari Andrea C. , Atatüre Mete 
Published: May 2017

AbstractQuantum light emitters have been observed in atomically thin layers of transition metal dichalcogenides. However, they are found at random locations within the host material and usually in low densities, hindering experiments aiming to investigate this new class of emitters. Here, we create deterministic arrays of hundreds of quantum emitters in tungsten diselenide and tungsten disulphide monolayers, emitting across a range of wavelengths in the visible spectrum (610–680 nm and 740–820 nm), with a greater spectral stability than their randomly occurring counterparts. This is achieved by depositing monolayers onto silica substrates nanopatterned with arrays of 150-nm-diameter pillars ranging from 60 to 190 nm in height. The nanopillars create localized deformations in the material resulting in the quantum confinement of excitons. Our method may enable the placement of emitters in photonic structures such as optical waveguides in a scalable way, where precise and accurate positioning is paramount.
Shifting the optimal stiffness for cell migration
Authors: Bangasser Benjamin L. , Shamsan Ghaidan A. , Chan Clarence E. , Opoku Kwaku N. , Tüzel Erkan , Schlichtmann Benjamin W. , Kasim Jesse A. , Fuller Benjamin J. , McCullough Brannon R. , Rosenfeld Steven S. , Odde David J. 
Published: May 2017

AbstractCell migration, which is central to many biological processes including wound healing and cancer progression, is sensitive to environmental stiffness, and many cell types exhibit a stiffness optimum, at which migration is maximal. Here we present a cell migration simulator that predicts a stiffness optimum that can be shifted by altering the number of active molecular motors and clutches. This prediction is verified experimentally by comparing cell traction and F-actin retrograde flow for two cell types with differing amounts of active motors and clutches: embryonic chick forebrain neurons (ECFNs; optimum ∼1 kPa) and U251 glioma cells (optimum ∼100 kPa). In addition, the model predicts, and experiments confirm, that the stiffness optimum of U251 glioma cell migration, morphology and F-actin retrograde flow rate can be shifted to lower stiffness by simultaneous drug inhibition of myosin II motors and integrin-mediated adhesions.
Hit and go CAS9 delivered through a lentiviral based self-limiting circuit
Authors: Petris Gianluca , Casini Antonio , Montagna Claudia , Lorenzin Francesca , Prandi Davide , Romanel Alessandro , Zasso Jacopo , Conti Luciano , Demichelis Francesca , Cereseto Anna 
Published: May 2017

AbstractIn vivo application of the CRISPR-Cas9 technology is still limited by unwanted Cas9 genomic cleavages. Long-term expression of Cas9 increases the number of genomic loci non-specifically cleaved by the nuclease. Here we develop a Self-Limiting Cas9 circuit for Enhanced Safety and specificity (SLiCES) which consists of an expression unit for Streptococcus pyogenes Cas9 (SpCas9), a self-targeting sgRNA and a second sgRNA targeting a chosen genomic locus. The self-limiting circuit results in increased genome editing specificity by controlling Cas9 levels. For its in vivo utilization, we next integrate SLiCES into a lentiviral delivery system (lentiSLiCES) via circuit inhibition to achieve viral particle production. Upon delivery into target cells, the lentiSLiCES circuit switches on to edit the intended genomic locus while simultaneously stepping up its own neutralization through SpCas9 inactivation. By preserving target cells from residual nuclease activity, our hit and go system increases safety margins for genome editing.
Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq
Authors: Wang Kaile , Lai Shujuan , Yang Xiaoxu , Zhu Tianqi , Lu Xuemei , Wu Chung-I , Ruan Jue 
Published: May 2017

AbstractDetection of de novo, low-frequency mutations is essential for characterizing cancer genomes and heterogeneous cell populations. However, the screening capacity of current ultrasensitive NGS methods is inadequate owing to either low-efficiency read utilization or severe amplification bias. Here, we present o2n-seq, an ultrasensitive and high-efficiency NGS library preparation method for discovering de novo, low-frequency mutations. O2n-seq reduces the error rate of NGS to 10−5–10−8. The efficiency of its data usage is about 10–30 times higher than that of barcode-based strategies. For detecting mutations with allele frequency (AF) 1% in 4.6 Mb-sized genome, the sensitivity and specificity of o2n-seq reach to 99% and 98.64%, respectively. For mutations with AF around 0.07% in phix174, o2n-seq detects all the mutations with 100% specificity. Moreover, we successfully apply o2n-seq to screen de novo, low-frequency mutations in human tumours. O2n-seq will aid to characterize the landscape of somatic mutations in research and clinical settings.
Tomographic active optical trapping of arbitrarily shaped objects by exploiting 3D refractive index maps
Authors: Kim Kyoohyun , Park YongKeun 
Published: May 2017

AbstractOptical trapping can manipulate the three-dimensional (3D) motion of spherical particles based on the simple prediction of optical forces and the responding motion of samples. However, controlling the 3D behaviour of non-spherical particles with arbitrary orientations is extremely challenging, due to experimental difficulties and extensive computations. Here, we achieve the real-time optical control of arbitrarily shaped particles by combining the wavefront shaping of a trapping beam and measurements of the 3D refractive index distribution of samples. Engineering the 3D light field distribution of a trapping beam based on the measured 3D refractive index map of samples generates a light mould, which can manipulate colloidal and biological samples with arbitrary orientations and/or shapes. The present method provides stable control of the orientation and assembly of arbitrarily shaped particles without knowing a priori information about the sample geometry. The proposed method can be directly applied in biophotonics and soft matter physics.
Short single-stranded DNA degradation products augment the activation of Toll-like receptor 9
Authors: Pohar Jelka , Lainšček Duško , Ivičak-Kocjan Karolina , Cajnko Miša-Mojca , Jerala Roman , Benčina Mojca 
Published: May 2017

AbstractToll-like receptors encounter a diversity of degradation products in endosomes. TLR7 and TLR8 have been shown to be activated by RNA degradation products. Here we show that although TLR9 requires single-stranded DNA longer than 20 nucleotides for a robust response, TLR9 activation is augmented by CpG-containing oligodeoxyribonucleotides (sODNs) as short as 2 nucleotides, which, by themselves, do not induce activation in cell cultures, as well as in mice. sODNs also activate human TLR9 in combination with ODNs containing a single CpG motif that by themselves do not activate human TLR9. The specific sequence motif of sODN and colocalization of ODN and sODN suggest that the mechanism of activation involves binding of both ODN and sODN to TLR9. sODNs augment TLR9 activation by mammalian genomic DNA indicating the role of short DNA degradation products in the endosomes in response to infection or in autoimmune disease, particularly at limiting concentrations of ODNs.
Interface-driven formation of a two-dimensional dodecagonal fullerene quasicrystal
Authors: Paßens M. , Caciuc V. , Atodiresei N. , Feuerbacher M. , Moors M. , Dunin-Borkowski R. E. , Blügel S. , Waser R. , Karthäuser S. 
Published: May 2017

AbstractSince their discovery, quasicrystals have attracted continuous research interest due to their unique structural and physical properties. Recently, it was demonstrated that dodecagonal quasicrystals could be used as bandgap materials in next-generation photonic devices. However, a full understanding of the formation mechanism of quasicrystals is necessary to control their physical properties. Here we report the formation of a two-dimensional dodecagonal fullerene quasicrystal on a Pt3Ti(111) surface, which can be described in terms of a square–triangle tiling. Employing density functional theory calculations, we identify the complex adsorption energy landscape of the Pt-terminated Pt3Ti surface that is responsible for the quasicrystal formation. We demonstrate the presence of quasicrystal-specific phason strain, which provides the degree of freedom required to accommodate the quasicrystalline structure on the periodic substrate. Our results reveal detailed insight into an interface-driven formation mechanism and open the way to the creation of tailored fullerene quasicrystals with specific physical properties.
Artificial control of the bias-voltage dependence of tunnelling-anisotropic magnetoresistance using quantization in a single-crystal ferromagnet
Authors: Muneta Iriya , Kanaki Toshiki , Ohya Shinobu , Tanaka Masaaki 
Published: May 2017

AbstractA major issue in the development of spintronic memory devices is the reduction of the power consumption for the magnetization reversal. For this purpose, the artificial control of the magnetic anisotropy of ferromagnetic materials is of great importance. Here, we demonstrate the control of the carrier-energy dependence of the magnetic anisotropy of the density of states (DOS) using the quantum size effect in a single-crystal ferromagnetic material, GaMnAs. We show that the mainly twofold symmetry of the magnetic anisotropy of DOS, which is attributed to the impurity band, is changed to a fourfold symmetry by enhancing the quantum size effect in the valence band of the GaMnAs quantum wells. By combination with the gate electric-field control technique, our concept of the usage of the quantum size effect for the control of the magnetism will pave the way for the ultra-low-power manipulation of magnetization in future spintronic devices.
Long-range ferrimagnetic order in a two-dimensional supramolecular Kondo lattice
Authors: Girovsky Jan , Nowakowski Jan , Ali Md. Ehesan , Baljozovic Milos , Rossmann Harald R. , Nijs Thomas , Aeby Elise A. , Nowakowska Sylwia , Siewert Dorota , Srivastava Gitika , Wäckerlin Christian , Dreiser Jan , Decurtins Silvio , Liu Shi-Xia , Oppeneer Peter M. , Jung Thomas A. , Ballav Nirmalya 
Published: May 2017

AbstractRealization of long-range magnetic order in surface-supported two-dimensional systems has been challenging, mainly due to the competition between fundamental magnetic interactions as the short-range Kondo effect and spin-stabilizing magnetic exchange interactions. Spin-bearing molecules on conducting substrates represent a rich platform to investigate the interplay of these fundamental magnetic interactions. Here we demonstrate the direct observation of long-range ferrimagnetic order emerging in a two-dimensional supramolecular Kondo lattice. The lattice consists of paramagnetic hexadeca-fluorinated iron phthalocyanine (FeFPc) and manganese phthalocyanine (MnPc) molecules co-assembled into a checkerboard pattern on single-crystalline Au(111) substrates. Remarkably, the remanent magnetic moments are oriented in the out-of-plane direction with significant contribution from orbital moments. First-principles calculations reveal that the FeFPc-MnPc antiferromagnetic nearest-neighbour coupling is mediated by the Ruderman–Kittel–Kasuya–Yosida exchange interaction via the Au substrate electronic states. Our findings suggest the use of molecular frameworks to engineer novel low-dimensional magnetically ordered materials and their application in molecular quantum devices.
pSILAC mass spectrometry reveals ZFP91 as IMiD-dependent substrate of the CRL4CRBN ubiquitin ligase
Authors: An Jian , Ponthier Charles M. , Sack Ragna , Seebacher Jan , Stadler Michael B. , Donovan Katherine A. , Fischer Eric S. 
Published: May 2017

AbstractThalidomide and its derivatives lenalidomide and pomalidomide (IMiDs) are effective treatments of haematologic malignancies. It was shown that IMiDs impart gain-of-function properties to the CUL4-RBX1-DDB1-CRBN (CRL4CRBN) ubiquitin ligase that enable binding, ubiquitination and degradation of key therapeutic targets such as IKZF1, IKZF3 and CSNK1A1. While these substrates have been implicated as efficacy targets in multiple myeloma (MM) and 5q deletion associated myelodysplastic syndrome (del(5q)-MDS), other targets likely exist. Using a pulse-chase SILAC mass spectrometry-based proteomics approach, we demonstrate that lenalidomide induces the ubiquitination and degradation of ZFP91. We establish ZFP91 as a bona fide IMiD-dependent CRL4CRBN substrate and further show that ZFP91 harbours a zinc finger (ZnF) motif, related to the IKZF1/3 ZnF, critical for IMiD-dependent CRBN binding. These findings demonstrate that single time point pulse-chase SILAC mass spectrometry-based proteomics (pSILAC MS) is a sensitive approach for target identification of small molecules inducing selective protein degradation.
Spin injection and helicity control of surface spin photocurrent in a three dimensional topological insulator
Authors: Huang Y. Q. , Song Y. X. , Wang S. M. , Buyanova I. A. , Chen W. M. 
Published: May 2017

AbstractA three-dimensional (3D) topological insulator (TI) is a unique quantum phase of matter with exotic physical properties and promising spintronic applications. However, surface spin current in a common 3D TI remains difficult to control and the out-of-plane spin texture is largely unexplored. Here, by means of surface spin photocurrent in Bi2Te3 TI devices driven by circular polarized light, we identify the subtle effect of the spin texture of the topological surface state including the hexagonal warping term on the surface current. By exploring the out-of-plane spin texture, we demonstrate spin injection from GaAs to TI and its significant contribution to the surface current, which can be manipulated by an external magnetic field. These discoveries pave the way to not only intriguing new physics but also enriched spin functionalities by integrating TI with conventional semiconductors, such that spin-enabled optoelectronic devices may be fabricated in such hybrid structures.
Deep sleep maintains learning efficiency of the human brain
Authors: Fattinger Sara , de Beukelaar Toon T. , Ruddy Kathy L. , Volk Carina , Heyse Natalie C. , Herbst Joshua A. , Hahnloser Richard H. R. , Wenderoth Nicole , Huber Reto 
Published: May 2017

AbstractIt is hypothesized that deep sleep is essential for restoring the brain’s capacity to learn efficiently, especially in regions heavily activated during the day. However, causal evidence in humans has been lacking due to the inability to sleep deprive one target area while keeping the natural sleep pattern intact. Here we introduce a novel approach to focally perturb deep sleep in motor cortex, and investigate the consequences on behavioural and neurophysiological markers of neuroplasticity arising from dedicated motor practice. We show that the capacity to undergo neuroplastic changes is reduced by wakefulness but restored during unperturbed sleep. This restorative process is markedly attenuated when slow waves are selectively perturbed in motor cortex, demonstrating that deep sleep is a requirement for maintaining sustainable learning efficiency.
A canonical neural mechanism for behavioral variability
Authors: Darshan Ran , Wood William E. , Peters Susan , Leblois Arthur , Hansel David 
Published: May 2017

AbstractThe ability to generate variable movements is essential for learning and adjusting complex behaviours. This variability has been linked to the temporal irregularity of neuronal activity in the central nervous system. However, how neuronal irregularity actually translates into behavioural variability is unclear. Here we combine modelling, electrophysiological and behavioural studies to address this issue. We demonstrate that a model circuit comprising topographically organized and strongly recurrent neural networks can autonomously generate irregular motor behaviours. Simultaneous recordings of neurons in singing finches reveal that neural correlations increase across the circuit driving song variability, in agreement with the model predictions. Analysing behavioural data, we find remarkable similarities in the babbling statistics of 5–6-month-old human infants and juveniles from three songbird species and show that our model naturally accounts for these ‘universal’ statistics.
Understanding trends in electrochemical carbon dioxide reduction rates
Authors: Liu Xinyan , Xiao Jianping , Peng Hongjie , Hong Xin , Chan Karen , Nørskov Jens K. 
Published: May 2017

AbstractElectrochemical carbon dioxide reduction to fuels presents one of the great challenges in chemistry. Herein we present an understanding of trends in electrocatalytic activity for carbon dioxide reduction over different metal catalysts that rationalize a number of experimental observations including the selectivity with respect to the competing hydrogen evolution reaction. We also identify two design criteria for more active catalysts. The understanding is based on density functional theory calculations of activation energies for electrochemical carbon monoxide reduction as a basis for an electrochemical kinetic model of the process. We develop scaling relations relating transition state energies to the carbon monoxide adsorption energy and determine the optimal value of this descriptor to be very close to that of copper.
MicroRNAs 146a/b-5 and 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes
Authors: Lopez Juan Pablo , Fiori Laura M. , Cruceanu Cristiana , Lin Rixing , Labonte Benoit , Cates Hannah M. , Heller Elizabeth A. , Vialou Vincent , Ku Stacy M. , Gerald Christophe , Han Ming-Hu , Foster Jane , Frey Benicio N. , Soares Claudio N. , Müller Daniel J. , Farzan Faranak , Leri Francesco , MacQueen Glenda M. , Feilotter Harriet , Tyryshkin Kathrin , Evans Kenneth R. , Giacobbe Peter , Blier Pierre , Lam Raymond W. , Milev Roumen , Parikh Sagar V. , Rotzinger Susan , Strother Steven C. , Lewis Cathryn M. , Aitchison Katherine J. , Wittenberg Gayle M. , Mechawar Naguib , Nestler Eric J. , Uher Rudolf , Kennedy Sidney H. , Turecki Gustavo 
Published: May 2017

AbstractAntidepressants (ADs) are the most common treatment for major depressive disorder (MDD). However, only ∼30% of patients experience adequate response after a single AD trial, and this variability remains poorly understood. Here, we investigated microRNAs (miRNAs) as biomarkers of AD response using small RNA-sequencing in paired samples from MDD patients enrolled in a large, randomized placebo-controlled trial of duloxetine collected before and 8 weeks after treatment. Our results revealed differential expression of miR-146a-5p, miR-146b-5p, miR-425-3p and miR-24-3p according to treatment response. These results were replicated in two independent clinical trials of MDD, a well-characterized animal model of depression, and post-mortem human brains. Furthermore, using a combination of bioinformatics, mRNA studies and functional in vitro experiments, we showed significant dysregulation of genes involved in MAPK/Wnt signalling pathways. Together, our results indicate that these miRNAs are consistent markers of treatment response and regulators of the MAPK/Wnt systems.
Polymorphisms of the oxytocin receptor gene and overeating: the intermediary role of endophenotypic risk factors
Authors: Davis C , Patte K , Zai C , Kennedy J L 
Published: May 2017

Abstract
Background/Objectives:
Oxytocin (OXT) is an evolutionarily ancient neuropeptide with strong links to affiliative and prosocial behaviors, and the management of stress. Increases in OXT also tend to decrease food intake, especially of sweet carbohydrates. The social correlates of low OXT levels mesh with the social deficits and stress proneness identified in interpersonal models of overeating, as well as the increased appetite for highly palatable foods typically seen in chronic overeaters. The objectives of this study were to investigate links between polymorphisms of the oxytocin receptor (OXTR) gene and overeating, and to examine OXTR links with relevant endophenotypes of overeating related to reward and stress sensitivity, and to food preferences.

Subject/Methods:
The sample comprised 460 adults between the ages of 25 and 50 years recruited from the community, and representing a broad range of body weights. Overeating, reward and punishment sensitivity, and food preferences, were quantified as composite variables using well-validated questionnaires. In addition, seven single-nucleotide polymorphisms (rs237878, rs237885, rs2268493, rs2268494, rs2254298, rs53576, rs2268498) of the OXTR gene were genotyped.

Results:
Analyses identified a four-marker haplotype that was significantly related to food preferences. Individual genotype analyses also found that at least one of the markers was related to each of the phenotypic variables. In addition, an empirically derived structural equation model linking genetic and phenotype variables produced a good fit to the data.

Conclusions:
The results of this preliminary study have demonstrated that OXTR variation is associated with overeating, and with endophenotypic traits such as sweet and fatty food preferences, and reward and punishment sensitivity. In general, the genetic findings also favor the view that overeating may be associated with relatively low basal OXT levels.