Glory Oscillations in the Index of Refraction for Matter-Waves

We have measured the index of refraction for sodium de Broglie waves in gases of Ar, Kr, Xe, and nitrogen over a wide range of sodium velocities. We observe glory oscillations -- a velocity-dependent oscillation in the forward scattering amplitude. An atom interferometer was used to observe glory oscillations in the phase shift caused by the collision, which are larger than glory oscillations observed in the cross section. The glory oscillations depend sensitively on the shape of the interatomic potential, allowing us to discriminate among various predictions for these potentials, none of which completely agrees with our measurements

Array atomic force microscopy for real-time multiparametric analysis.

Nanoscale multipoint structure-function analysis is essential for deciphering the complexity of multiscale biological and physical systems. Atomic force microscopy (AFM) allows nanoscale structure-function imaging in various operating environments and can be integrated seamlessly with disparate probe-based sensing and manipulation technologies. Conventional AFMs only permit sequential single-point analysis; widespread adoption of array AFMs for simultaneous multipoint study is challenging owing to the intrinsic limitations of existing technological approaches. Here, we describe a prototype dispersive optics-based array AFM capable of simultaneously monitoring multiple probe-sample interactions. A single supercontinuum laser beam is utilized to spatially and spectrally map multiple cantilevers, to isolate and record beam deflection from individual cantilevers using distinct wavelength selection. This design provides a remarkably simplified yet effective solution to overcome the optical cross-talk while maintaining subnanometer sensitivity and compatibility with probe-based sensors. We demonstrate the versatility and robustness of our system on parallel multiparametric imaging at multiscale levels ranging from surface morphology to hydrophobicity and electric potential mapping in both air and liquid, mechanical wave propagation in polymeric films, and the dynamics of living cells. This multiparametric, multiscale approach provides opportunities for studying the emergent properties of atomic-scale mechanical and physicochemical interactions in a wide range of physical and biological networks

Functional Liquid Metal Nanoparticles Produced by Liquid-Based Nebulization

Functional liquid metal nanoparticles (NPs), produced from eutectic alloys of gallium, promise new horizons in the fields of sensors, microfluidics, flexible electronics, catalysis, and biomedicine. Here, the development of a vapor cavity generating ultrasonic platform for nebulizing liquid metal within aqueous media for the one-step production of stable and functional liquid metal NPs is shown. The size distribution of the NPs is fully characterized and it is demonstrated that various macro and small molecules can also be grafted onto these liquid metal NPs during the liquid-based nebulization process. The cytotoxicity of the NPs grafted with different molecules is further explored. Moreover, it is shown that it is possible to control the thickness of the oxide layer on the produced NPs using electrochemistry that can be embedded within the platform. It is envisaged that this platform can be adapted as a cost-effective and versatile device for the rapid production of functional liquid metal NPs for future liquid metal-based optical, electronic, catalytic, and biomedical applications

Irony Detection in Twitter: The Role of Affective Content

© ACM 2016. This is the author's version of the work. It is posted here for your personal use. Not for redistribution. The definitive Version of Record was published in ACM Transactions on Internet Technology, Vol. 16. http://dx.doi.org/10.1145/2930663.[EN] Irony has been proven to be pervasive in social media, posing a challenge to sentiment analysis systems. It is a creative linguistic phenomenon where affect-related aspects play a key role. In this work, we address the problem of detecting irony in tweets, casting it as a classification problem. We propose a novel model that explores the use of affective features based on a wide range of lexical resources available for English, reflecting different facets of affect. Classification experiments over different corpora show that affective information helps in distinguishing among ironic and nonironic tweets. Our model outperforms the state of the art in almost all cases.The National Council for Science and Technology (CONACyT Mexico) has funded the research work of Delia Irazu Hernandez Farias (Grant No. 218109/313683 CVU-369616). The work of Viviana Patti was partially carried out at the Universitat Politecnica de Valencia within the framework of a fellowship of the University of Turin cofunded by Fondazione CRT (World Wide Style Program 2). The work of Paolo Rosso has been partially funded by the SomEMBED TIN2015-71147-C2-1-P MINECO research project and by the Generalitat Valenciana under the grant ALMAMATER (PrometeoII/2014/030).Hernandez-Farias, DI.; Patti, V.; Rosso, P. (2016). Irony Detection in Twitter: The Role of Affective Content. ACM Transactions on Internet Technology. 16(3):19:1-19:24. https://doi.org/10.1145/2930663S19:119:24163Rob Abbott, Marilyn Walker, Pranav Anand, Jean E. Fox Tree, Robeson Bowmani, and Joseph King. 2011. 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Quadrature Strategies for Constructing Polynomial Approximations

Finding suitable points for multivariate polynomial interpolation and approximation is a challenging task. Yet, despite this challenge, there has been tremendous research dedicated to this singular cause. In this paper, we begin by reviewing classical methods for finding suitable quadrature points for polynomial approximation in both the univariate and multivariate setting. Then, we categorize recent advances into those that propose a new sampling approach and those centered on an optimization strategy. The sampling approaches yield a favorable discretization of the domain, while the optimization methods pick a subset of the discretized samples that minimize certain objectives. While not all strategies follow this two-stage approach, most do. Sampling techniques covered include subsampling quadratures, Christoffel, induced and Monte Carlo methods. Optimization methods discussed range from linear programming ideas and Newton's method to greedy procedures from numerical linear algebra. Our exposition is aided by examples that implement some of the aforementioned strategies

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Broad Epigenetic Signature of Maternal Care in the Brain of Adult Rats

BACKGROUND: Maternal care is associated with long-term effects on behavior and epigenetic programming of the NR3C1 (GLUCOCORTICOID RECEPTOR) gene in the hippocampus of both rats and humans. In the rat, these effects are reversed by cross-fostering, demonstrating that they are defined by epigenetic rather than genetic processes. However, epigenetic changes at a single gene promoter are unlikely to account for the range of outcomes and the persistent change in expression of hundreds of additional genes in adult rats in response to differences in maternal care. METHODOLOGY/PRINCIPAL FINDINGS: We examine here using high-density oligonucleotide array the state of DNA methylation, histone acetylation and gene expression in a 7 million base pair region of chromosome 18 containing the NR3C1 gene in the hippocampus of adult rats. Natural variations in maternal care are associated with coordinate epigenetic changes spanning over a hundred kilobase pairs. The adult offspring of high compared to low maternal care mothers show epigenetic changes in promoters, exons, and gene ends associated with higher transcriptional activity across many genes within the locus examined. Other genes in this region remain unchanged, indicating a clustered yet specific and patterned response. Interestingly, the chromosomal region containing the protocadherin-α, -β, and -γ (Pcdh) gene families implicated in synaptogenesis show the highest differential response to maternal care. CONCLUSIONS/SIGNIFICANCE: The results suggest for the first time that the epigenetic response to maternal care is coordinated in clusters across broad genomic areas. The data indicate that the epigenetic response to maternal care involves not only single candidate gene promoters but includes transcriptional and intragenic sequences, as well as those residing distantly from transcription start sites. These epigenetic and transcriptional profiles constitute the first tiling microarray data set exploring the relationship between epigenetic modifications and RNA expression in both protein coding and non-coding regions across a chromosomal locus in the mammalian brain