bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local probe of single phonon dynamics in warm ion crystals
Authors: Abdelrahman A. , Khosravani O. , Gessner M. , Buchleitner A. , Breuer H. -P. , Gorman D. , Masuda R. , Pruttivarasin T. , Ramm M. , Schindler P. , Häffner H. 
Published: June 2017

AbstractThe detailed characterization of non-trivial coherence properties of composite quantum systems of increasing size is an indispensable prerequisite for scalable quantum computation, as well as for understanding non-equilibrium many-body physics. Here, we show how autocorrelation functions in an interacting system of phonons as well as the quantum discord between distinct degrees of freedoms can be extracted from a small controllable part of the system. As a benchmark, we show this in chains of up to 42 trapped ions, by tracing a single phonon excitation through interferometric measurements of only a single ion in the chain. We observe the spreading and partial refocusing of the excitation in the chain, even on a background of thermal excitations. We further show how this local observable reflects the dynamical evolution of quantum discord between the electronic state and the vibrational degrees of freedom of the probe ion.
Constriction of the mitochondrial inner compartment is a priming event for mitochondrial division
Authors: Cho Bongki , Cho Hyo Min , Jo Youhwa , Kim Hee Dae , Song Myungjae , Moon Cheil , Kim Hyongbum , Kim Kyungjin , Sesaki Hiromi , Rhyu Im Joo , Kim Hyun , Sun Woong 
Published: June 2017

AbstractMitochondrial division is critical for the maintenance and regulation of mitochondrial function, quality and distribution. This process is controlled by cytosolic actin-based constriction machinery and dynamin-related protein 1 (Drp1) on mitochondrial outer membrane (OMM). Although mitochondrial physiology, including oxidative phosphorylation, is also important for efficient mitochondrial division, morphological alterations of the mitochondrial inner-membrane (IMM) have not been clearly elucidated. Here we report spontaneous and repetitive constriction of mitochondrial inner compartment (CoMIC) associated with subsequent division in neurons. Although CoMIC is potentiated by inhibition of Drp1 and occurs at the potential division spots contacting the endoplasmic reticulum, it appears on IMM independently of OMM. Intra-mitochondrial influx of Ca2+ induces and potentiates CoMIC, and leads to K+-mediated mitochondrial bulging and depolarization. Synergistically, optic atrophy 1 (Opa1) also regulates CoMIC via controlling Mic60-mediated OMM–IMM tethering. Therefore, we propose that CoMIC is a priming event for efficient mitochondrial division.
A covalent PIN1 inhibitor selectively targets cancer cells by a dual mechanism of action
Authors: Campaner Elena , Rustighi Alessandra , Zannini Alessandro , Cristiani Alberto , Piazza Silvano , Ciani Yari , Kalid Ori , Golan Gali , Baloglu Erkan , Shacham Sharon , Valsasina Barbara , Cucchi Ulisse , Pippione Agnese Chiara , Lolli Marco Lucio , Giabbai Barbara , Storici Paola , Carloni Paolo , Rossetti Giulia , Benvenuti Federica , Bello Ezia , D’Incalci Maurizio , Cappuzzello Elisa , Rosato Antonio , Del Sal Giannino 
Published: June 2017

AbstractThe prolyl isomerase PIN1, a critical modifier of multiple signalling pathways, is overexpressed in the majority of cancers and its activity strongly contributes to tumour initiation and progression. Inactivation of PIN1 function conversely curbs tumour growth and cancer stem cell expansion, restores chemosensitivity and blocks metastatic spread, thus providing the rationale for a therapeutic strategy based on PIN1 inhibition. Notwithstanding, potent PIN1 inhibitors are still missing from the arsenal of anti-cancer drugs. By a mechanism-based screening, we have identified a novel covalent PIN1 inhibitor, KPT-6566, able to selectively inhibit PIN1 and target it for degradation. We demonstrate that KPT-6566 covalently binds to the catalytic site of PIN1. This interaction results in the release of a quinone-mimicking drug that generates reactive oxygen species and DNA damage, inducing cell death specifically in cancer cells. Accordingly, KPT-6566 treatment impairs PIN1-dependent cancer phenotypes in vitro and growth of lung metastasis in vivo.
Centromeres are maintained by fastening CENP-A to DNA and directing an arginine anchor-dependent nucleosome transition
Authors: Guo Lucie Y. , Allu Praveen Kumar , Zandarashvili Levani , McKinley Kara L. , Sekulic Nikolina , Dawicki-McKenna Jennine M. , Fachinetti Daniele , Logsdon Glennis A. , Jamiolkowski Ryan M. , Cleveland Don W. , Cheeseman Iain M. , Black Ben E. 
Published: June 2017

AbstractMaintaining centromere identity relies upon the persistence of the epigenetic mark provided by the histone H3 variant, centromere protein A (CENP-A), but the molecular mechanisms that underlie its remarkable stability remain unclear. Here, we define the contributions of each of the three candidate CENP-A nucleosome-binding domains (two on CENP-C and one on CENP-N) to CENP-A stability using gene replacement and rapid protein degradation. Surprisingly, the most conserved domain, the CENP-C motif, is dispensable. Instead, the stability is conferred by the unfolded central domain of CENP-C and the folded N-terminal domain of CENP-N that becomes rigidified 1,000-fold upon crossbridging CENP-A and its adjacent nucleosomal DNA. Disrupting the ‘arginine anchor’ on CENP-C for the nucleosomal acidic patch disrupts the CENP-A nucleosome structural transition and removes CENP-A nucleosomes from centromeres. CENP-A nucleosome retention at centromeres requires a core centromeric nucleosome complex where CENP-C clamps down a stable nucleosome conformation and CENP-N fastens CENP-A to the DNA.
Temperature-regulated guest admission and release in microporous materials
Authors: Li Gang , Shang Jin , Gu Qinfen , Awati Rohan V. , Jensen Nathan , Grant Andrew , Zhang Xueying , Sholl David S. , Liu Jefferson Z. , Webley Paul A. , May Eric F. 
Published: June 2017

AbstractWhile it has long been known that some highly adsorbing microporous materials suddenly become inaccessible to guest molecules below certain temperatures, previous attempts to explain this phenomenon have failed. Here we show that this anomalous sorption behaviour is a temperature-regulated guest admission process, where the pore-keeping group’s thermal fluctuations are influenced by interactions with guest molecules. A physical model is presented to explain the atomic-level chemistry and structure of these thermally regulated micropores, which is crucial to systematic engineering of new functional materials such as tunable molecular sieves, gated membranes and controlled-release nanocontainers. The model was validated experimentally with H2, N2, Ar and CH4 on three classes of microporous materials: trapdoor zeolites, supramolecular host calixarenes and metal-organic frameworks. We demonstrate how temperature can be exploited to achieve appreciable hydrogen and methane storage in such materials without sustained pressure. These findings also open new avenues for gas sensing and isotope separation.
A two-dimensional Dirac fermion microscope
Authors: Bøggild Peter , Caridad José M. , Stampfer Christoph , Calogero Gaetano , Papior Nick Rübner , Brandbyge Mads 
Published: June 2017

AbstractThe electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots.
Neural correlates of evidence accumulation during value-based decisions revealed via simultaneous EEG-fMRI
Authors: Pisauro M. Andrea , Fouragnan Elsa , Retzler Chris , Philiastides Marios G. 
Published: June 2017

AbstractCurrent computational accounts posit that, in simple binary choices, humans accumulate evidence in favour of the different alternatives before committing to a decision. Neural correlates of this accumulating activity have been found during perceptual decisions in parietal and prefrontal cortex; however the source of such activity in value-based choices remains unknown. Here we use simultaneous EEG–fMRI and computational modelling to identify EEG signals reflecting an accumulation process and demonstrate that the within- and across-trial variability in these signals explains fMRI responses in posterior-medial frontal cortex. Consistent with its role in integrating the evidence prior to reaching a decision, this region also exhibits task-dependent coupling with the ventromedial prefrontal cortex and the striatum, brain areas known to encode the subjective value of the decision alternatives. These results further endorse the proposition of an evidence accumulation process during value-based decisions in humans and implicate the posterior-medial frontal cortex in this process.
Different populations of CD11b+ dendritic cells drive Th2 responses in the small intestine and colon
Authors: Mayer Johannes U. , Demiri Mimoza , Agace William W. , MacDonald Andrew S. , Svensson-Frej Marcus , Milling Simon W. 
Published: June 2017

AbstractT-helper 2 (Th2) cell responses defend against parasites. Although dendritic cells (DCs) are vital for the induction of T-cell responses, the DC subpopulations that induce Th2 cells in the intestine are unidentified. Here we show that intestinal Th2 responses against Trichuris muris worms and Schistosoma mansoni eggs do not develop in mice with IRF-4-deficient DCs (IRF-4f/f CD11c-cre). Adoptive transfer of conventional DCs, in particular CD11b-expressing DCs from the intestine, is sufficient to prime S. mansoni-specific Th2 responses. Surprisingly, transferred IRF-4-deficient DCs also effectively prime S. mansoni-specific Th2 responses. Egg antigens do not induce the expression of IRF-4-related genes. Instead, IRF-4f/f CD11c-cre mice have fewer CD11b+ migrating DCs and fewer DCs carrying parasite antigens to the lymph nodes. Furthermore, CD11b+CD103+ DCs induce Th2 responses in the small intestine, whereas CD11b+CD103− DCs perform this role in the colon, revealing a specific functional heterogeneity among intestinal DCs in inducing Th2 responses.
Reactivation of associative structure specific outcome responses during prospective evaluation in reward-based choices
Authors: Wang Maya Zhe , Hayden Benjamin Y. 
Published: June 2017

AbstractBefore making a reward-based choice, we must evaluate each option. Some theories propose that prospective evaluation involves a reactivation of the neural response to the outcome. Others propose that it calls upon a response pattern that is specific to each underlying associative structure. We hypothesize that these views are reconcilable: during prospective evaluation, offers reactivate neural responses to outcomes that are unique to each associative structure; when the outcome occurs, this pattern is activated, simultaneously, with a general response to the reward. We recorded single-units from macaque orbitofrontal cortex (Area 13) in a riskless choice task with interleaved described and experienced offer trials. Here we report that neural activations to offers and their outcomes overlap, as do neural activations to the outcomes on the two trial types. Neural activations to experienced and described offers are unrelated even though they predict the same outcomes. Our reactivation theory parsimoniously explains these results.
TIP30 regulates lipid metabolism in hepatocellular carcinoma by regulating SREBP1 through the Akt/mTOR signaling pathway
Authors: Yin F , Sharen G , Yuan F , Peng Y , Chen R , Zhou X , Wei H , Li B , Jing W , Zhao J 
Published: June 2017

AbstractLipid reprogramming has been considered as a crucial characteristic in hepatocellular carcinoma (HCC) initiation and progression. However, detailed molecular mechanisms have yet to be clearly defined. Here, we examined the effects of tumor suppressor TIP30 on the regulation of HCC lipid metabolism. We found that decreased TIP30 expression leads to elevated fatty acid synthesis and enhanced levels of lipogenic enzymes SCD and FASN in HCC cells. Moreover, SREBP1 is one of the key transcription factors regulating liver lipid metabolism, and TIP30 deficiency significantly increased SREBP1 expression and nuclear accumulation. Small interfering RNAs targeting SREBP1 could reverse fatty acid synthesis induced by TIP30 deficiency. Furthermore, downregulating TIP30 activated the Akt/mTOR signaling pathway to upregulate SREBP1 expression, which promoted lipid metabolism by activating gene transcription of lipogenesis, including fasn and scd. We also showed that TIP30 deficiency-regulated lipid metabolism promoted proliferation of HCC cells. Clinically, our data revealed that TIP30 expression significantly correlated with SREBP1 in patients with HCC and that a combination of TIP30 and SREBP1 is a powerful predictor of HCC prognosis. Together, our data suggested a novel function of TIP30 in HCC progression and indicate that TIP30 regulation of SREBP1 may represent a novel target for HCC treatment.
Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass
Authors: Byrne Stephen L. , Conaghan Patrick , Barth Susanne , Arojju Sai Krishna , Casler Michael , Michel Thibauld , Velmurugan Janaki , Milbourne Dan 
Published: June 2017

AbstractPrior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, which has a time and labour cost. It can also be inferred from family means, although the spread in days to heading within families demands roguing in first generation synthetics. Another option is to predict heading date from molecular markers. In this study we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Opportunities exist to develop a cheap assay to sequence a small number of regions in linkage disequilibrium with heading date QTL in thousands of samples. Simultaneous use of these markers in non-linkage based marker-assisted selection approaches, such as paternity testing, should enhance the utility of such an approach.
High-Risk Human Papillomavirus E7 Alters Host DNA Methylome and Represses HLA-E Expression in Human Keratinocytes
Authors: Cicchini Louis , Blumhagen Rachel Z. , Westrich Joseph A. , Myers Mallory E. , Warren Cody J. , Siska Charlotte , Raben David , Kechris Katerina J. , Pyeon Dohun 
Published: June 2017

AbstractHuman papillomavirus (HPV) infection distinctly alters methylation patterns in HPV-associated cancer. We have recently reported that HPV E7-dependent promoter hypermethylation leads to downregulation of the chemokineCXCL14and suppression of antitumor immune responses. To investigate the extent of gene expression dysregulated by HPV E7-induced DNA methylation, we analyzed parallel global gene expression and DNA methylation using normal immortalized keratinocyte lines, NIKS, NIKS-16, NIKS-18, and NIKS-16∆E7. We show that expression of the MHC class I genes is downregulated in HPV-positive keratinocytes in an E7-dependent manner. Methylome analysis revealed hypermethylation at a distal CpG island (CGI) near theHLA-Egene in NIKS-16 cells compared to either NIKS cells or NIKS-16∆E7 cells, which lack E7 expression. TheHLA-ECGI functions as an active promoter element which is dramatically repressed by DNA methylation. HLA-E protein expression on cell surface is downregulated by high-risk HPV16 and HPV18 E7 expression, but not by low-risk HPV6 and HPV11 E7 expression. Conversely, demethylation at theHLA-ECGI restores HLA-E protein expression in HPV-positive keratinocytes. Because HLA-E plays an important role in antiviral immunity by regulating natural killer and CD8+T cells, epigenetic downregulation ofHLA-Eby high-risk HPV E7 may contribute to virus-induced immune evasion during HPV persistence.
Ferroelectric-assisted gold nanoparticles array for centimeter-scale highly reproducible SERS substrates
Authors: Liu Xiaoyan , Osada Minoru , Kitamura Kenji , Nagata Takahiro , Si Donghui 
Published: June 2017

AbstractAssemble metal nanoparticles into various ordered structures with scale up to centimeter area is required to meet diverse needs of lab-on-a-chips and analytic components. Here, we present the uniform and high-yield fabrication of centimeter-scale gold nanoparticles (AuNPs) array for SERS substrates. Ferroelectric-assisted assembly of AuNPs line array is successfully fabricated by using a periodically poled LiNbO3 (PPLN) single crystal as a template. SNOM-Raman shows that the uniform assembly of AuNPs exhibits a high density of “hot spots” arising from strong electromagnetic (EM) field coupling induced by adjacent AuNPs. Quantitative analysis based on SERS detection describes an excellent reproducibility with an intensity variation less than 7% at 1649 cm−1 of Rhodamine 6G. SERS spectra combined with 3D-FDTD modelling indicate that the EM enhancement occurs at all three excitation wavelength of 515, 561 and 633 nm and the 561-nm-laser displays the strongest Raman enhancement with an enhancement factor in an order of 109. The corresponding experimental and theoretical results present a new strategy to fabricate large-area, highly reproducible and sensitive SERS substrates for practical applications.
Behavioural and physiological responses to prey-related cues reflect higher competitiveness of invasive vs. native ladybirds
Authors: Rondoni Gabriele , Ielo Fulvio , Ricci Carlo , Conti Eric 
Published: June 2017

AbstractUnderstanding the traits that might be linked with biological invasions represents a great challenge for preventing non-target effects on local biodiversity. In predatory insects, the ability to exploit habitats for oviposition and the physiological response to prey availability differs between species. Those species that respond more readily to environmental changes may confer to their offspring a competitive advantage over other species. Here, we tested the hypothesis that the invasive Harmonia axyridis (Coleoptera: Coccinellidae) makes better use of information from a plant-prey (Vicia faba - Aphis fabae) system compared to the native Oenopia conglobata. Y-tube olfactometer bioassays revealed that both species used olfactory cues from the system, but H. axyridis exhibited a more complete response. This species was also attracted by plants previously infested by aphids, indicating the capacity to exploit volatile synomones induced in plants by aphid attack. Oocyte resorption was investigated when different olfactory stimuli were provided under prey shortage and the readiness of new oogenesis was measured when prey was available again. H. axyridis exhibited higher plasticity in oogenesis related to the presence/absence of plant-aphid volatiles. Our results support the hypothesis that H. axyridis is more reactive than O. conglobata to olfactory cues from the plant-prey system.
A Sensory Material Approach for Reducing Variability in Additively Manufactured Metal Parts
Authors: Franco B. E. , Ma J. , Loveall B. , Tapia G. A. , Karayagiz K. , Liu J. , Elwany A. , Arroyave R. , Karaman I. 
Published: June 2017

AbstractDespite the recent growth in interest for metal additive manufacturing (AM) in the biomedical and aerospace industries, variability in the performance, composition, and microstructure of AM parts remains a major impediment to its widespread adoption. The underlying physical mechanisms, which cause variability, as well as the scale and nature of variability are not well understood, and current methods are ineffective at capturing these details. Here, a Nickel-Titanium alloy is used as a sensory material in order to quantitatively, and rather rapidly, observe compositional and/or microstructural variability in selective laser melting manufactured parts; thereby providing a means to evaluate the role of process parameters on the variability. We perform detailed microstructural investigations using transmission electron microscopy at various locations to reveal the origins of microstructural variability in this sensory material. This approach helped reveal how reducing the distance between adjacent laser scans below a critical value greatly reduces both the in-sample and sample-to-sample variability. Microstructural investigations revealed that when the laser scan distance is wide, there is an inhomogeneity in subgrain size, precipitate distribution, and dislocation density in the microstructure, responsible for the observed variability. These results provide an important first step towards understanding the nature of variability in additively manufactured parts.
Highly conductive nano-sized Magnéli phases titanium oxide (TiOx)
Authors: Arif Aditya F. , Balgis Ratna , Ogi Takashi , Iskandar Ferry , Kinoshita Akihiro , Nakamura Keitaro , Okuyama Kikuo 
Published: June 2017

AbstractDespite the strong recent revival of Magnéli phase TiOx as a promising conductive material, synthesis of Magnéli phase TiOx nanoparticles has been a challenge because of the heavy sintering nature of TiO2 at elevated temperatures. We have successfully synthesized chain-structured Magnéli phases TiOx with diameters under 30 nm using a thermal-induced plasma process. The synthesized nanoparticles consisted of a mixture of several Magnéli phases. A post-synthesis heat-treatment was performed to reduce the electrical resistivity without changing the particle morphology. The resistivity of the heat-treated particle was as low as 0.04 Ω.cm, with a specific surface area of 52.9 m2 g−1. The effects of heat-treatment on changes in the crystal structure and their correlation with the electron conductivity are discussed based on transmission electron microscopy images, X-ray diffraction spectra, and X-ray adsorption fine structure spectra. Electrochemical characterization using cyclic voltammetry and potentiodynamic scan shows a remarkable electrochemical stability in a strongly oxidizing environment.