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417 results on '"Bromberg Y."'

2. Control of coherent backscattering by breaking optical reciprocity

Author

Bromberg, Y., Redding, B., Popoff, S. M., and Cao, H.

Subjects
Physics - Optics, Quantum Physics
Abstract

Reciprocity is a universal principle that has a profound impact on many areas of physics. A fundamental phenomenon in condensed-matter physics, optical physics and acoustics, arising from reciprocity, is the constructive interference of quantum or classical waves which propagate along time-reversed paths in disordered media, leading to, for example, weak localization and metal-insulator transition. Previous studies have shown that such coherent effects are suppressed when reciprocity is broken. Here we show that by breaking reciprocity in a controlled manner, we can tune, rather than simply suppress, these phenomena. In particular, we manipulate coherent backscattering of light, also known as weak localization. By utilizing a non-reciprocal magneto-optical effect, we control the interference between time-reversed paths inside a multimode fiber with strong mode mixing, and realize a continuous transition from the well-known peak to a dip in the backscattered intensity. Our results may open new possibilities for coherent control of classical and quantum waves in complex systems, Comment: Comments are welcome

Published
2015
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3. Critical States Embedded in the Continuum

Author

Koirala, M., Yamilov, A., Basiri, A., Bromberg, Y., Cao, H., and Kottos, T.

Subjects
Condensed Matter - Disordered Systems and Neural Networks, Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Optics
Abstract

We introduce a class of critical states which are embedded in the continuum (CSC) of one-dimensional optical waveguide array with one non-Hermitian defect. These states are at the verge of being fractal and have real propagation constant. They emerge at a phase transition which is driven by the imaginary refractive index of the defect waveguide and it is accompanied by a mode segregation which reveals analogies with the Dicke super -radiance. Below this point the states are extended while above they evolve to exponentially localized modes. An addition of a background gain or loss can turn these localized states to bound states in the continuum., Comment: 4.5 pages, 3 figures, 1 page of supplementary material including one figure

Published
2014
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4. Light Localization induced by Random Imaginary Permittivities

Author

Basiri, A., Bromberg, Y., Yamilov, A., Cao, H., and Kottos, T.

Subjects
Condensed Matter - Disordered Systems and Neural Networks, Physics - Optics
Abstract

We show the emergence of light localization in arrays of coupled optical waveguides with randomness only in the imaginary part of their permittivity and develop a one-parameter scaling theory for the normalized participation number of the Floquet-Bloch modes. This localization introduces a new length scale in the decay of the autocorrelation function of a paraxial beam propagation. Our results are relevant to a vast family of systems with randomness in the dissipative part of their impedance spatial profile., Comment: five pages plus two pages of supplementary material

Published
2014
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5. Hanbury Brown and Twiss Correlations of Anderson Localized Waves

Author

Lahini, Y., Bromberg, Y., Shechtman, Y., Szameit, A., Christodoulides, D. N., Morandotti, R., and Silberberg, Y.

Subjects
Condensed Matter - Disordered Systems and Neural Networks
Abstract

When light waves propagate through disordered photonic lattices, they can eventually become localized due to multiple scattering effects. Here we show experimentally that while the evolution and localization of the photon density distribution is similar in the two cases of diagonal and off-diagonal disorder, the density-density correlation carries a distinct signature of the type of disorder. We show that these differences reflect a symmetry in the spectrum and eigenmodes that exists in off-diagonally disordered lattices but is absent in lattices with diagonal disorder., Comment: 4 pages, 3 figures, comments welcome

Published
2011
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6. Quantum and classical correlations in waveguide lattices

Author

Bromberg, Y., Lahini, Y., Morandotti, R., and Silberberg, Y.

Subjects
Quantum Physics
Abstract

We study quantum and classical Hanbury Brown-Twiss correlations in waveguide lattices. We develop a theory for the propagation of photon pairs in the lattice, predicting the emergence of nontrivial quantum interferences unique to lattice systems. Experimentally, we observe the classical counterpart of these interferences using intensity correlation measurements. We discuss the correspondence between the classical and quantum correlations, and consider path-entangled input states which do not have a classical analogue. Our results demonstrate that waveguide lattices can be used as a robust and highly controllable tool for manipulating quantum states, and offer new ways of studying the quantum properties of light., Comment: Comments are welcome

Published
2008
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9. PredictProtein - Predicting Protein Structure and Function for 29 Years.

Author

Bernhofer, M., Dallago, C., Karl, T., Satagopam, V., Heinzinger, M., Littmann, M., Olenyi, T., Qiu, J., Schütze, K., Yachdav, G., Ashkenazy, H., Ben-Tal, N., Bromberg, Y., Goldberg, T., Kajan, L., O'Donoghue, S., Sander, C., Schafferhans, A., Schlessinger, A., Vriend, G., Mirdita, M., Gawron, P., Gu, W., Jarosz, Y., Trefois, C., Steinegger, M., Schneider, R., Rost, B., Bernhofer, M., Dallago, C., Karl, T., Satagopam, V., Heinzinger, M., Littmann, M., Olenyi, T., Qiu, J., Schütze, K., Yachdav, G., Ashkenazy, H., Ben-Tal, N., Bromberg, Y., Goldberg, T., Kajan, L., O'Donoghue, S., Sander, C., Schafferhans, A., Schlessinger, A., Vriend, G., Mirdita, M., Gawron, P., Gu, W., Jarosz, Y., Trefois, C., Steinegger, M., Schneider, R., and Rost, B.

Abstract

Contains fulltext : 244283.pdf (Publisher’s version ) (Open Access), Since 1992 PredictProtein (https://predictprotein.org) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre for Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. PredictProtein was the first Internet server for protein predictions. It pioneered combining evolutionary information and machine learning. Given a protein sequence as input, the server outputs multiple sequence alignments, predictions of protein structure in 1D and 2D (secondary structure, solvent accessibility, transmembrane segments, disordered regions, protein flexibility, and disulfide bridges) and predictions of protein function (functional effects of sequence variation or point mutations, Gene Ontology (GO) terms, subcellular localization, and protein-, RNA-, and DNA binding). PredictProtein's infrastructure has moved to the LCSB increasing throughput; the use of MMseqs2 sequence search reduced runtime five-fold (apparently without lowering performance of prediction methods); user interface elements improved usability, and new prediction methods were added. PredictProtein recently included predictions from deep learning embeddings (GO and secondary structure) and a method for the prediction of proteins and residues binding DNA, RNA, or other proteins. PredictProtein.org aspires to provide reliable predictions to computational and experimental biologists alike. All scripts and methods are freely available for offline execution in high-throughput settings.

Published
2021

12. Abstracts of oral presentations

Author

Boulieu, R., Lenoir, A., Mornex, J. F., Bohman, C., Balzarini, J., Wigerinck, P., Van Aerschot, A., Herdewijn, P., De Clercq, Erik, Brosh, S., Zoref-Shani, E., Sperling, O., Danziger, E., Sidi, Y., Bromberg, Y., Burgemeister, Renate, Rötzer, Elke, Gutensohn, Wolf, Connolly, G. P., Harrison, P. J., Diasio, R. B., Lu, Z., Zhang, R., Gresser, U., Gutensohn, W., Resta, R., Thompson, L. F., Javaux, F., Vincent, M. F., Van den Berghe, G., Kamilli, I., Rauch, R., Hahn, D., Keuzenkamp-Jansen, C. W., De Abreu, R. A., Bökkerink, J. P. M., vd Heijden, M. A. H., Löffler, M., Becker, C., Wegerie, E., Marcussen, M., Overgaard-Hansen, K., Klenow, H., Marinaki, A. M., Harley, E. H., McBride, M. B., Simmonds, H. A., Moro, F., Cameron, J. S., Ogg, C. S., Williams, D. G., Rigden, S., Haycock, G., Miranda, M. E., Puig, J. G., Mateos, F. A., Vázquez, J. O., van Haperen, V. W. T. Ruiz, Veerman, G., Vermorken, J. B., Peters, G. J., van der Wilt, C. L., Noordhuis, P., Smid, K., Pinedo, H. M., Salerno, C., Lomonte, A., Giardini, O., Crifo, C., Smolenski, R. T., Yacoub, M. H., Seymour, A. M. -L., Stegmann, A. P. A., Honders, M. W., Willemze, R., Landegent, J. E., Stet, E. H., Vogels-Mentink, G. M., Lambooy, L. H. J., Trijbels, J. M. F., Torres, R. J., Tozzi, M. G., Pesi, R., Turriani, M., Allegrini, S., Camici, M., Ipata, P. L., van den Berg, A. A., Meinsma, J. R., van Lenthe, H., van Gennip, A. H., van Kuilenburg, A. B. P., Abeling, N. G. G. M., Bakker, H. D., Slingerland, R. J., Van den Bergh, F., and Sabina, R. L.

Published
1993
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13. A collaborative strategy for mitigating tracking through browser fingerprinting

Author

Gómez-Boix, A., Frey, D., Bromberg, Y. -D, Baudry, Benoit, Gómez-Boix, A., Frey, D., Bromberg, Y. -D, and Baudry, Benoit

Abstract

Browser fingerprinting is a technique that collects information about the browser configuration and the environment in which it is running. This information is so diverse that it can partially or totally identify users online. Over time, several countermeasures have emerged to mitigate tracking through browser fingerprinting. However, these measures do not offer full coverage in terms of privacy protection, as some of them may introduce inconsistencies or unusual behaviors, making these users stand out from the rest. We address these limitations by proposing a novel approach that minimizes both the identifiability of users and the required changes to browser configuration. To this end, we exploit clustering algorithms to identify the devices that are prone to share the same or similar fingerprints and to provide them with a new non-unique fingerprint. We then use this fingerprint to automatically assemble and run web browsers through virtualization within a docker container. Thus all the devices in the same cluster will end up running a web browser with an indistinguishable and consistent fingerprint., QC 20200327

Published
2019
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14. On-chip quantum frequency combs

Author

Reimer, C., Kues, M., Roztocki, P., Grazioso, F., Johnston, T., Morandotti, R., Wetzel, B., Little, B.E., Chu, S.T., Moss, D.J., Bromberg, Y., and Caspani, L.

Subjects
QC350
Published
2016

16. Signature-based clustering for analysis of the wound microbiome

Author

Hu, X, Yoo, I, Gao, J, Gong, Y, Shyu, C R, Zheng, J H, Korkin, D, Bromberg, Y, Chappell, Timothy, Geva, Shlomo, Hogan, Jim, Huygens, Flavia, Kelly, Wayne, Perrin, Dimitri, Hu, X, Yoo, I, Gao, J, Gong, Y, Shyu, C R, Zheng, J H, Korkin, D, Bromberg, Y, Chappell, Timothy, Geva, Shlomo, Hogan, Jim, Huygens, Flavia, Kelly, Wayne, and Perrin, Dimitri

Abstract

Chronic wounds present a significant risk to the patient and a substantial drain on health budgets, with the problem likely to worsen markedly with increased incidence of type II diabetes. The wound fluid microbiome is known to influence wound healing outcomes, but is poorly characterised. Next Generation Sequencing approaches yield abundant data from wound samples, but progress in understanding these microbial communities may be hampered by the speed of existing analysis pipelines and limitations on coverage by 16S databases. This paper presents SigClust, a novel clustering method based on binary signatures derived from sequence reads. SigClust yields superior cluster coherence and separation of metagenomic read data in timeframes substantially reduced from those of alternative methods. We demonstrate its utility in the wound context on a preliminary set of labelled patient data. We show how a time course analysis based on tracking the dominant clusters over successive wound samples can identify markers of both successful wound healing and wounds refractory to treatment. Clusters prominent in these analyses are found to correspond to bacterial species known to be implicated as a determinant of wound outcomes, notably a number of strains of Staphylococcus aureus. The clusters obtained rapidly via SigClust support improved understanding of the wound microbiome without direct reliance on a reference database, offering the promise of a SigClust-based pipeline for wound analysis and prediction, and potentially novel methods for wound treatment and management.

Published
2017

17. THCluster: Herb Supplements Categorization for Precision Traditional Chinese Medicine

Author

Hu, XH, Shyu, CR, Bromberg, Y, Gao, J, Gong, Y, Korkin, D, Yoo, I, Zheng, JH, Ruan, C, Wang, Y, Zhang, Y, Ma, J, Chen, H, Aickelin, U, Zhu, S, Zhang, T, Hu, XH, Shyu, CR, Bromberg, Y, Gao, J, Gong, Y, Korkin, D, Yoo, I, Zheng, JH, Ruan, C, Wang, Y, Zhang, Y, Ma, J, Chen, H, Aickelin, U, Zhu, S, and Zhang, T

Abstract

There has been a continuing demand for traditional and complementary medicine worldwide. A fundamental and important topic in Traditional Chinese Medicine (TCM) is to optimize the prescription and to detect herb regularities from TCM data. In this paper, we propose a novel clustering model to solve this general problem of herb categorization, a pivotal task of prescription optimization and herb regularities. The model utilizes Random Walks method, Bayesian rules and Expectation Maximization(EM) models to complete a clustering analysis effectively on a heterogeneous information network. We performed extensive experiments on the real-world datasets and compared our method with other algorithms and experts. Experimental results have demonstrated the effectiveness of the proposed model for discovering useful categorization of herbs and its potential clinical manifestations.

Published
2017

20. PredictProtein--an open resource for online prediction of protein structural and functional features

Author

Yachdav, G., Kloppmann, E., Kajan, L., Hecht, M., Goldberg, T., Hamp, T., Honigschmid, P., Schafferhans, A., Roos, M., Bernhofer, M., Richter, L., Ashkenazy, H., Punta, M., Schlessinger, A., Bromberg, Y., Schneider, R., Vriend, G., Sander, C., Ben-Tal, N., and Rost, B.

Subjects
Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19]
Abstract

Contains fulltext : 136025.pdf (Publisher’s version ) (Open Access) PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein-protein binding sites (ISIS2), protein-polynucleotide binding sites (SomeNA) and predictions of the effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics. To this end, the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures. The web server and sources are available at http://ppopen.rostlab.org.

Published
2014

21. Preface

Author

Giacomello, Alessandro, Peters, G. J., Eriksson, Staffan, De Abreu, Ronney, Kristensen, T., Munch-Petersen, B., Vincenzetti, S., Cambi, A., Neuhard, J., Garattini, E., Vita, A., Oka, J., Matsumoto, A., Hosokawa, Y., Inoue, S., Allegrini, S., Johnson, R. B., Fiol, C. J., Eriksson, S., Fabianowska-Majewska, K., Wasiak, T., Duley, J., Simmonds, A., Bretner, M., Felczak, K., Poznański, J., Dzik, J. M., Golos, B., Jarmuła, A., Rode, W., Kulikowski, T., Codacci-Pisanelli, G., Pinedo, H. M., Noordhuis, P., van Groeningen, C. J., van der Wilt, C. L., Franchi, F., Hatse, S., Balzarini, J., De Clercq, E., Marinello, E., Rosi, F., Dispensa, E., Mangiavacchi, P., Riario-Sforza, G., Agostinho, A. B., Smolenski, R. T., Müller, Mathias M., Roch-Ramel, F., Guisan, B., Diezi, J., Tavenier, M., Skladanowski, A. C., de Abreu, R. A., de Jong, J. W., Åmellem, Øystein, Löffler, Monika, Pettersen, Erik O., Boulieu, R., Lenoir, A., Bertocchi, M., Mornex, J. F., Makarewicz, W., Spychala J., Mitchell B. S., Barankiewcz J., Góra-Tybor, Joanna, Robak, Tadeusz, Spasokukotskaja T., Sasvári-Székely M., Piróth Zs., Kazimierczuk Z., Staub M., Keuzenkamp-Jansen, C W, De Abreu, R A, Bökkerink, J P M, Trijbels, J M F, Eriksson S., Warzocha, K., Krykowski, E., Góra-Tybor, J., Fronczak, A., Robak, T., Minelli, A., Moroni, M., Monacelli, N., Mezzasoma, I., Amici, A., Emanuelli, M., Raffaelli, N., Ruggieri, S., Magni, G., Carta, M. C., Mattana, A., Poddie, F., Sgarrella, F., Tozzi, M. G., Veerman, G., Ruiz van Haperen, V. W. T., van Moorsel, C. J. A., Pesi, R., Baiocchi, C., Camici, M., Ipata, P. L., Kozłowska, M., Świerczyński, J., Smoleński, R. T., Jastorff, B., Messina, E., Savini, F., Procopio, A., Giacomello, A., Wielgus-Kutrowska, B., Kulikowska, E., Wierzchowski, J., Bzowska, A., Shugar, D., Fairbanks, Lynette D, Ruckemann, Katarzyna, Simmonds, H Anne, Kaletha, K., Szymańska, G., Thebault, M., Raffin, J. P., Le Gal, Y., Griesmacher, Andrea, De Abreu, Ronney A., Zych, M., Ruckemann, K., Jagodzinski, P., Kochan, Z., Stolk, J., Boerbooms, A., De Abreu, R., de Koning, D., van de Putte, L., Fiorini, M., Bazzichi, L., Bertolini, G., Martini, C., Ciompi, M. L., Lucacchini, A., Pizzichini, M., Terzuoli, L., Arezzini, L., Fe, L., Pagani, R., Miscetti, P., Allegrucci, C., Sebesta, I., Duley, J. A., Simmonds, H. A., Gross, M., Salerno, C., Stone, T. W., Van den Berghe, G., Valik, Dalibor, Jones, James D., Guerranti, R., Fè, L., Sforza, G. Riario, Knecht, Wolfgang, Grein, Klaus, Lodi, R., Iotti, S., Barbiroli, B., Bonin, B., Chantin, C., Bory, C., Micheli, V., Jacomelli, G., Morozzi, G., Fioravanti, A., Marcolongo, R., Pompucci, G., Peters G J, Noordhuis P, Komissarov A, Holwerda U, Kok R M, Van Laar J A M, Van der Wilt C L, Van Groeningen C J, Pinedo H M, Perrett, David, Jacobsson, Bengt, Sisto A., Iezzi A., Di Carlo M., Pizzigallo E., Akhondzadeh, S., MacGregor, D. G., Ogilvy, H. V., Zoref-Shani, E., Brosh, S., Sidi, Y., Bromberg, Y., Sperling, O., van Gennip, A. H., Abeling, N. G. G. M., Stroomer, A. E. M., van Lenthe, H., Bakker, H. D., van Kuilenburg, A. B. P., Connolly, G. P., Abbott, N. J., Lilling, G., Gozes, I., Vreken, P., Meinsma, R., de Ahreu, R. A., Diasio, R. B., Albin, N., Johnson, M. R., Shahinian, H., Wang, K., Gathof, B. S., Rocchigiani, M., Puig, J. G., Mateos, F., Sestini, S., Krijt, J., Shin, Y., Gresser, U., Costa, A., Maximova, N., Andolina, M., Paci, M., Carrozzi, M., Osbich, A., Durighello, M., Cavalli, F., Geatti, O., Zammarchi, E., Morgan, Gareth, Webster, A. D. B., Slavin, S., Naparstek, E., Nagler, A., Acker, M., Cividalli, G., Kapellushnik, Y., Varadi, G., Ben-Yoseph, R., Or, R., Parfenov, V. V., Ignatenko, M. A., Amchenkova, A. M., Narovlyansky, A. N., Spoto, G., Mastropasqua, L., Gizzi, F., Arduini, A., Del Gallo, P., Ciancaglini, M., Gallenga, P. E., Šebesta, I., Zeman, J., Crifò, C., Di Vito, M., Lomonte, A., Gerber, G., Carlucci, F., Tabucchi, A., Vannoni P., Di Pietro M. C., Vincent, M. F., Bontemps, F., Boer, P., Rötzer, E., Ehrmann, D., Empl, W., Bride, M. B. Mc, Ogg, C. S., Cameron, J. S., Moro, F., Rigden, S., Rees, L., Hoff, W. Van't, Raman, V., Palmieri, P., Mastropierro, G., Albertazzi, A., Rucci, C., Darlington, L. G., Cotton, S. R., de Gorter, J. J., Lawrence, E. S., Petrie, A., Sarsam, R. P., Semple, M. J., Warburton, E. A., Quaratino, C. P., Talone, L., Di Sciascio, N., Hrebíček, M. H., Poupětová, H., Ledvinová, J., Elleder, M., Vondrák, K., Rees, P. C., Wonke, B., Thein, S. L., Clegg, J. B., Marlewski, M., Pennelli, A., Di Marzio, M., Angelini, G., Sabatino, G., de Koning, P., Kerstens, P., de Graaf, R., Hayek, G., and Cardona, F.

Published
1995
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26. Protocole de découverte de services interopérable en réseau ad hoc

Author

Sailhan, Francoise, Bromberg, Y?rom-David, Issarny, Val?rie, Centre d'études et de recherche en informatique et communications (CEDRIC), Ecole Nationale Supérieure d'Informatique pour l'Industrie et l'Entreprise (ENSIIE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), CEDRIC. Réseaux et Objets Connectés (CEDRIC - ROC), and Ecole Nationale Supérieure d'Informatique pour l'Industrie et l'Entreprise (ENSIIE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Ecole Nationale Supérieure d'Informatique pour l'Industrie et l'Entreprise (ENSIIE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)

Subjects
[INFO]Computer Science [cs], [INFO.INFO-ES]Computer Science [cs]/Embedded Systems, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2009

32. The young PI buzz: Learning from the organizers of the junior principal investigator meeting at ISMB-ECCB 2013

Author

de Ridder, J. (author), Bromberg, Y (author), Michaut, M (author), Satagopam, VP (author), Corpas, M (author), Macintyre, G (author), Alexandrov, T (author), de Ridder, J. (author), Bromberg, Y (author), Michaut, M (author), Satagopam, VP (author), Corpas, M (author), Macintyre, G (author), and Alexandrov, T (author)

Abstract

Pattern Recognition and Bioinformatics

Published
2013
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41. Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study

Author

Calton, M. A., primary, Ersoy, B. A., additional, Zhang, S., additional, Kane, J. P., additional, Malloy, M. J., additional, Pullinger, C. R., additional, Bromberg, Y., additional, Pennacchio, L. A., additional, Dent, R., additional, McPherson, R., additional, Ahituv, N., additional, and Vaisse, C., additional

Published
2009
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