bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photon-efficient imaging with a single-photon camera
Authors: Shin Dongeek , Xu Feihu , Venkatraman Dheera , Lussana Rudi , Villa Federica , Zappa Franco , Goyal Vivek K. , Wong Franco N. C. , Shapiro Jeffrey H. 
Published: June 2016

AbstractReconstructing a scene’s 3D structure and reflectivity accurately with an active imaging system operating in low-light-level conditions has wide-ranging applications, spanning biological imaging to remote sensing. Here we propose and experimentally demonstrate a depth and reflectivity imaging system with a single-photon camera that generates high-quality images from ∼1 detected signal photon per pixel. Previous achievements of similar photon efficiency have been with conventional raster-scanning data collection using single-pixel photon counters capable of ∼10-ps time tagging. In contrast, our camera’s detector array requires highly parallelized time-to-digital conversions with photon time-tagging accuracy limited to ∼ns. Thus, we develop an array-specific algorithm that converts coarsely time-binned photon detections to highly accurate scene depth and reflectivity by exploiting both the transverse smoothness and longitudinal sparsity of natural scenes. By overcoming the coarse time resolution of the array, our framework uniquely achieves high photon efficiency in a relatively short acquisition time.
Prediction of pressure-promoted thermal rejuvenation in metallic glasses
Authors: Miyazaki Narumasa , Wakeda Masato , Wang Yun-Jiang , Ogata Shigenobu 
Published: June 2016

AbstractRejuvenation is the structural excitation of glassy materials, and is a promising approach for improving the macroscopic deformability of metallic glasses. This atomistic study proposes the application of compressive hydrostatic pressure during the glass-forming quenching process and demonstrates highly rejuvenated glass states that have not been attainable without the application of pressure. Surprisingly, the pressure-promoted rejuvenation process increases the characteristic short- and medium-range order, even though it leads to a higher-energy glassy state. This ‘local order’–‘energy’ relation is completely opposite to conventional thinking regarding the relation, suggesting the presence of a well-ordered high-pressure glass/high-energy glass phase. We also demonstrate that the rejuvenated glass made by the pressure-promoted rejuvenation exhibits greater plastic performance than as-quenched glass, and greater strength and stiffness than glass made without the application of pressure. It is thus possible to tune the mechanical properties of glass using the pressure-promoted rejuvenation technique.
No-cloning of quantum steering
Authors: Chiu Ching-Yi , Lambert Neill , Liao Teh-Lu , Nori Franco , Li Che-Ming 
Published: June 2016

AbstractEinstein–Podolsky–Rosen (EPR) steering allows two parties to verify their entanglement, even if one party’s measurements are untrusted. This concept has not only provided new insights into the nature of non-local spatial correlations in quantum mechanics, but also serves as a resource for one-sided device-independent quantum information tasks. Here, we investigate how EPR steering behaves when one-half of a maximally entangled pair of qudits (multidimensional quantum systems) is cloned by a universal cloning machine. We find that EPR steering, as verified by a criterion based on the mutual information between qudits, can only be found in one of the copy subsystems but not both. We prove that this is also true for the single-system analogue of EPR steering. We find that this restriction, which we term ‘no-cloning of quantum steering’, elucidates the physical reason why steering can be used to secure sources and channels against cloning-based attacks when implementing quantum communication and quantum computation protocols.
Targeting duplex DNA with the reversible reactivity of quinone methides
Authors: Huang Chengyun , Liu Yang , Rokita Steven E 
Published: June 2016

AbstractDNA alkylation and crosslinking remains a common and effective strategy for anticancer chemotherapy despite its infamous lack of specificity. Coupling a reactive group to a sequence-directing component has the potential to enhance target selectivity but may suffer from premature degradation or the need for an external signal for activation. Alternatively, quinone methide conjugates may be employed if they form covalent but reversible adducts with their sequence directing component. The resulting self-adducts transfer their quinone methide to a chosen target without an external signal and avoid off-target reactions by alternative intramolecular self-trapping. Efficient transfer is shown to depend on the nature of the quinone methide and the sequence-directing ligand in applications involving alkylation of duplex DNA through a triplex recognition motif. Success required an electron-rich derivative that enhanced the stability of the transient quinone methide intermediate and a polypyrimidine strand of DNA to associate with its cognate polypurine/polypyrimidine target. Related quinone methide conjugates with peptide nucleic acids were capable of quinone methide transfer from their initial precursor but not from their corresponding self-adduct. The active peptide nucleic acid derivatives were highly selective for their complementary target.
The anti-angiogenic effect and novel mechanisms of action of Combretastatin A-4
Authors: Su Min , Huang Jingjia , Liu Suyou , Xiao Yuhang , Qin Xiyuan , Liu Jia , Pi Chaoqiong , Luo Tiao , Li Jijia , Chen Xianghui , Luo Zhiyong 
Published: June 2016

AbstractCombretastatin A-4 (CA4) is the lead compound of a relatively new class of vascular disrupting agents that target existing tumor blood vessels. Recent studies showed the CA4 might inhibit angiogenesis. However, the underlying molecular mechanisms by which CA4 exerts its anti-angiogenic effects are not fully understood. In this study, we revealed that CA4 inhibited vascular endothelial growth factor (VEGF)-induced proliferation, migration and capillary-like tube formation of human umbilical vascular endothelial cells (HUVECs). In in vivo assay, CA4 suppressed neovascularization in chicken chorioallantoic membrane (CAM) model and decreased the microvessel density in tumor tissues of a breast cancer MCF-7 xenograft mouse model. In addition, CA4 decreased the expression level and secretion of VEGF both in MCF-7 cells and HUVECs under hypoxia, as well as the activation of VEGFR-2 and its downstream signaling mediators following VEGF stimulation in HUVECs. Moreover, VEGF and VEGFR-2 expression in tumor tissues of the mouse xenograft model were down-regulated following CA4 treatment. Taken together, results from the current work provide clear evidence that CA4 functions in endothelial cell system to inhibit angiogenesis, at least in part, by attenuating VEGF/VEGFR-2 signaling pathway.
An engineered tale-transcription factor rescues transcription of factor VII impaired by promoter mutations and enhances its endogenous expression in hepatocytes
Authors: Barbon Elena , Pignani Silvia , Branchini Alessio , Bernardi Francesco , Pinotti Mirko , Bovolenta Matteo 
Published: June 2016

AbstractTailored approaches to restore defective transcription responsible for severe diseases have been poorly explored. We tested transcription activator-like effectors fused to an activation domain (TALE-TFs) in a coagulation factor VII (FVII) deficiency model. In this model, the deficiency is caused by the −94C > G or −61T > G mutation, which abrogate the binding of Sp1 or HNF-4 transcription factors. Reporter assays in hepatoma HepG2 cells naturally expressing FVII identified a single TALE-TF (TF4) that, by targeting the region between mutations, specifically trans-activated both the variant (>100-fold) and wild-type (20–40-fold) F7 promoters. Importantly, in the genomic context of transfected HepG2 and transduced primary hepatocytes, TF4 increased F7 mRNA and protein levels (2- to 3-fold) without detectable off-target effects, even for the homologous F10 gene. The ectopic F7 expression in renal HEK293 cells was modestly affected by TF4 or by TALE-TF combinations. These results provide experimental evidence for TALE-TFs as gene-specific tools useful to counteract disease-causing promoter mutations.
Adaptive tuning functions arise from visual observation of past movement
Authors: Howard Ian S. , Franklin David W. 
Published: June 2016

AbstractVisual observation of movement plays a key role in action. For example, tennis players have little time to react to the ball, but still need to prepare the appropriate stroke. Therefore, it might be useful to use visual information about the ball trajectory to recall a specific motor memory. Past visual observation of movement (as well as passive and active arm movement) affects the learning and recall of motor memories. Moreover, when passive or active, these past contextual movements exhibit generalization (or tuning) across movement directions. Here we extend this work, examining whether visual motion also exhibits similar generalization across movement directions and whether such generalization functions can explain patterns of interference. Both the adaptation movement and contextual movement exhibited generalization beyond the training direction, with the visual contextual motion exhibiting much broader tuning. A second experiment demonstrated that this pattern was consistent with the results of an interference experiment where opposing force fields were associated with two separate visual movements. Overall, our study shows that visual contextual motion exhibits much broader (and shallower) tuning functions than previously seen for either passive or active movements, demonstrating that the tuning characteristics of past motion are highly dependent on their sensory modality.
Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain
Authors: Narayanan Sunilkumar Puthenpurackal , Nair Divya Gopalakrishnan , Schaal Daniel , Barbosa de Aguiar Marisa , Wenzel Sabine , Kremer Werner , Schwarzinger Stephan , Kalbitzer Hans Robert 
Published: June 2016

AbstractFatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23–230) as detected by [1H, 15N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn2+-binding to the octarepeat motif.
AurkA controls self-renewal of breast cancer-initiating cells promoting wnt3a stabilization through suppression of miR-128
Authors: Eterno V. , Zambelli A. , Villani L. , Tuscano A. , Manera S. , Spitaleri A. , Pavesi L. , Amato A. 
Published: June 2016

AbstractAurkA overexpression was previously found in breast cancer and associated to its ability in controlling chromosome segregation during mitosis, however whether it may affect breast cancer cells, endorsed with stem properties (BCICs), is still unclear. Surprisingly, a strong correlation between AurkA expression and β-catenin localization in breast cancer tissues suggested a link between AurkA and Wnt signaling. In our study, AurkA knock-down reduced wnt3a mRNA and suppressed metastatic signature of MDA-MB-231 cells. As a consequence, the amount of BCICs and their migratory capability dramatically decreased. Conversely, wnt3a mRNA stabilization and increased CD44+/CD24low/− subpopulation was found in AurkA-overexpressing MCF7 cells. In vivo, AurkA-overexpressing primary breast cancer cells showed higher tumorigenic properties. Interestingly, we found that AurkA suppressed the expression of miR-128, inhibitor of wnt3a mRNA stabilization. Namely, miR-128 suppression realized after AurkA binding to Snail. Remarkably, a strong correlation between AurkA and miR-128 expression in breast cancer tissues confirmed our findings. This study provides novel insights into an undisclosed role for the kinase AurkA in self-renewal and migration of BCICs affecting response to cancer therapies, metastatic spread and recurrence. In addition, it suggests a new therapeutic strategy taking advantage of miR-128 to suppress AurkA-Wnt3a signaling.
Maximal mid-expiratory flow is a surrogate marker of lung clearance index for assessment of adults with bronchiectasis
Authors: Guan Wei-jie , Yuan Jing-jing , Gao Yong-hua , Li Hui-min , Zheng Jin-ping , Chen Rong-chang , Zhong Nan-shan 
Published: June 2016

AbstractLittle is known about the comparative diagnostic value of lung clearance index (LCI) and maximal mid-expiratory flow (MMEF) in bronchiectasis. We compared the diagnostic performance, correlation and concordance with clinical variables, and changes of LCI and MMEF% predicted during bronchiectasis exacerbations (BEs). Patients with stable bronchiectasis underwent history inquiry, chest high-resolution computed tomography (HRCT), multiple-breath nitrogen wash-out test, spirometry and sputum culture. Patients who experienced BEs underwent these measurements during onset of BEs and 1 week following antibiotics therapy. Sensitivity analyses were performed in mild, moderate and severe bronchiectasis. We recruited 110 bronchiectasis patients between March 2014 and September 2015. LCI demonstrated similar diagnostic value with MMEF% predicted in discriminating moderate-to-severe from mild bronchiectasis. LCI negatively correlated with MMEF% predicted. Both parameters had similar concordance in reflecting clinical characteristics of bronchiectasis and correlated significantly with forced expiratory flow in one second, age, HRCT score, Pseudomonas aeruginosa colonization, cystic bronchiectasis, ventilation heterogeneity and bilateral bronchiectasis. In exacerbation cohort (n = 22), changes in LCI and MMEF% predicted were equally minimal during BEs and following antibiotics therapy. In sensitivity analyses, both parameters had similar diagnostic value and correlation with clinical variables. MMEF% predicted is a surrogate of LCI for assessing bronchiectasis severity.
Effect of curcumin analogs onα-synuclein aggregation and cytotoxicity
Authors: Jha Narendra Nath , Ghosh Dhiman , Das Subhadeep , Anoop Arunagiri , Jacob Reeba S. , Singh Pradeep K. , Ayyagari Narasimham , Namboothiri Irishi N. N. , Maji Samir K. 
Published: June 2016

AbstractAlpha-synuclein (α-Syn) aggregation into oligomers and fibrils is associated with dopaminergic neuron loss occurring in Parkinson’s disease (PD) pathogenesis. Compounds that modulate α-Syn aggregation and interact with preformed fibrils/oligomers and convert them to less toxic species could have promising applications in the drug development efforts against PD. Curcumin is one of the Asian food ingredient which showed promising role as therapeutic agent against many neurological disorders including PD. However, the instability and low solubility makes it less attractive for the drug development. In this work, we selected various curcumin analogs and studied their toxicity, stability and efficacy to interact with different α-Syn species and modulation of their toxicity. We found a subset of curcumin analogs with higher stability and showed that curcumin and its various analogs interact with preformed fibrils and oligomers and accelerate α-Syn aggregation to produce morphologically different amyloid fibrils in vitro. Furthermore, these curcumin analogs showed differential binding with the preformed α-Syn aggregates. The present data suggest the potential role of curcumin analogs in modulating α-Syn aggregation.
Mendelian Randomisation study of the influence of eGFR on coronary heart disease
Authors: Charoen Pimphen , Nitsch Dorothea , Engmann Jorgen , Shah Tina , White Jonathan , Zabaneh Delilah , Jefferis Barbara , Wannamethee Goya , Whincup Peter , Mulick Cassidy Amy , Gaunt Tom , Day Ian , McLachlan Stela , Price Jacqueline , Kumari Meena , Kivimaki Mika , Brunner Eric , Langenberg Claudia , Ben-Shlomo Yoav , Hingorani Aroon , Whittaker John , Pablo Casas Juan , Dudbridge Frank ,   the UCLEB Consortium, Dale Caroline , Finan Chris , Wong Andrew , Ong Ken , Drenos Fotios , Cooper Jackie , Sofat Reecha , Schmidt Floriaan , Lawlor Debbie A. , Talmud Philippa J. , Humphries Steve E. , Hardy Rebecca , Kuh Diana , Wareham Nicholas , Morris Richard , Plagno Vincent 
Published: June 2016

AbstractImpaired kidney function, as measured by reduced estimated glomerular filtration rate (eGFR), has been associated with increased risk of coronary heart disease (CHD) in observational studies, but it is unclear whether this association is causal or the result of confounding or reverse causation. In this study we applied Mendelian randomisation analysis using 17 genetic variants previously associated with eGFR to investigate the causal role of kidney function on CHD. We used 13,145 participants from the UCL-LSHTM-Edinburgh-Bristol (UCLEB) Consortium and 194,427 participants from the Coronary ARtery DIsease Genome-wide Replication and Meta-analysis plus Coronary Artery Disease (CARDIoGRAMplusC4D) consortium. We observed significant association of an unweighted gene score with CHD risk (odds ratio = 0.983 per additional eGFR-increasing allele, 95% CI = 0.970–0.996, p = 0.008). However, using weights calculated from UCLEB, the gene score was not associated with disease risk (p = 0.11). These conflicting results could be explained by a single SNP, rs653178, which was not associated with eGFR in the UCLEB sample, but has known pleiotropic effects that prevent us from drawing a causal conclusion. The observational association between low eGFR and increased CHD risk was not explained by potential confounders and there was no evidence of reverse causation, therefore leaving the remaining unexplained association as an open question.
The Phosphorylation and Distribution of Cortactin Downstream of Integrin α9β1 Affects Cancer Cell Behaviour
Authors: Høye Anette M. , Couchman John R. , Wewer Ulla M. , Yoneda Atsuko 
Published: June 2016

AbstractIntegrins, a family of heterodimeric adhesion receptors are implicated in cell migration, development and cancer progression. They can adopt conformations that reflect their activation states and thereby impact adhesion strength and migration. Integrins in an intermediate activation state may be optimal for migration and we have shown previously that fully activated integrin α9β1 corresponds with less migratory behaviour in melanoma cells. Here, we aimed to identify components associated with the activation status of α9β1. Using cancer cell lines with naturally occuring high levels of this integrin, activation by α9β1-specific ligands led to upregulation of fibronectin matrix assembly and tyrosine phosphorylation of cortactin on tyrosine 470 (Y470). Specifically, cortactin phosphorylated on Y470, but not Y421, redistributed together with α9β1 to focal adhesions where active β1 integrin also localises, upon integrin activation. This was commensurate with reduced migration. The localisation and phosphorylation of cortactin Y470 was regulated by Yes kinase and PTEN phosphatase. Cortactin levels influenced fibronectin matrix assembly and active β1 integrin on the cell surface, being inversely correlated with migratory behaviour. This study underlines the complex interplay between cortactin and α9β1 integrin that regulates cell-extracellular matrix interactions.
Enhanced optical gradient forces between coupled graphene sheets
Authors: Xu Xinbiao , Shi Lei , Liu Yang , Wang Zheqi , Zhang Xinliang 
Published: June 2016

AbstractOptical gradient forces between monolayer infinite-width graphene sheets as well as single-mode graphene nanoribbon pairs of graphene surface plasmons (GSPs) at mid-infrared frequencies were theoretically investigated. Although owing to the strongly enhanced optical field, the normalized optical force, fn, can reach 50 nN/μm/mW, which is the largest fn as we know, the propagation loss is also large. But we found that by changing the chemical potential of graphene, fn and the optical propagation loss can be balanced. The total optical force acted on the nanoribbon waveguides can thus enhance more than 1 order of magnitude than that in metallic surface plasmons (MSPs) waveguides with the same length and the loss can be lower. Owing to the enhanced optical force and the significant neff tuning by varying the chemical potential of graphene, we also propose an ultra-compact phase shifter.
The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
Authors: Lau Nyok-Sean , Makita Yuko , Kawashima Mika , Taylor Todd D. , Kondo Shinji , Othman Ahmad Sofiman , Shu-Chien Alexander Chong , Matsui Minami 
Published: June 2016

AbstractHevea brasiliensis Muell. Arg, a member of the family Euphorbiaceae, is the sole natural resource exploited for commercial production of high-quality natural rubber. The properties of natural rubber latex are almost irreplaceable by synthetic counterparts for many industrial applications. A paucity of knowledge on the molecular mechanisms of rubber biosynthesis in high yield traits still persists. Here we report the comprehensive genome-wide analysis of the widely planted H. brasiliensis clone, RRIM 600. The genome was assembled based on ~155-fold combined coverage with Illumina and PacBio sequence data and has a total length of 1.55 Gb with 72.5% comprising repetitive DNA sequences. A total of 84,440 high-confidence protein-coding genes were predicted. Comparative genomic analysis revealed strong synteny between H. brasiliensis and other Euphorbiaceae genomes. Our data suggest that H. brasiliensis’s capacity to produce high levels of latex can be attributed to the expansion of rubber biosynthesis-related genes in its genome and the high expression of these genes in latex. Using cap analysis gene expression data, we illustrate the tissue-specific transcription profiles of rubber biosynthesis-related genes, revealing alternative means of transcriptional regulation. Our study adds to the understanding of H. brasiliensis biology and provides valuable genomic resources for future agronomic-related improvement of the rubber tree.
Cross-stacked carbon nanotubes assisted self-separation of free-standing GaN substrates by hydride vapor phase epitaxy
Authors: Wei Tongbo , Yang Jiankun , Wei Yang , Huo Ziqiang , Ji Xiaoli , Zhang Yun , Wang Junxi , Li Jinmin , Fan Shoushan 
Published: June 2016

AbstractWe report a novel method to fabricate high quality 2-inch freestanding GaN substrate grown on cross-stacked carbon nanotubes (CSCNTs) coated sapphire by hydride vapor phase epitaxy (HVPE). As nanoscale masks, these CSCNTs can help weaken the interface connection and release the compressive stress by forming voids during fast coalescence and also block the propagation of threading dislocations (TDs). During the cool-down process, thermal stress-induced cracks are initiated at the CSCNTs interface with the help of air voids and propagated all over the films which leads to full self-separation of FS-GaN substrate. Raman and photoluminescence spectra further reveal the stress relief and crystalline improvement of GaN with CSCNTs. It is expected that the efficient, low cost and mass-producible technique may enable new applications for CNTs in nitride optoelectronic fields.