ALBERT

Description: : Development of effective tools such as oligo-microarrays and next-generation sequencing methods for monitoring gene expression on a large scale has resulted in the discovery of gene signatures with prognostic/predictive value in various malignant neoplastic diseases. However, with the exponential growth of gene expression databases, biologists are faced with the challenge of extracting useful information from these repositories. Here, we present a software package, BioPlat (Biomarkers Platform), which allows biologists to identify novel prognostic and predictive cancer biomarkers based on the data mining of gene expression signatures and gene expression profiling databases. BioPlat has been designed as an easy-to-use and flexible desktop software application, which provides a set of analytical tools related to data extraction, preprocessing, filtering, gene expression signature calculation, in silico validation, feature selection and annotation that leverage the integration and reuse of gene expression signatures in the context of follow-up data. Availability and implementation: BioPlat is a platform-independent software implemented in Java and supported on GNU/Linux and MS Windows, which is freely available for download at http://www.cancergenomics.net . Contact: mcabba@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Using data collected at the Pierre Auger Observatory during the past 3.7 years, we demonstrated a correlation between the arrival directions of cosmic rays with energy above 6 x 10(19) electron volts and the positions of active galactic nuclei (AGN) lying within approximately 75 megaparsecs. We rejected the hypothesis of an isotropic distribution of these cosmic rays with at least a 99% confidence level from a prescribed a priori test. The correlation we observed is compatible with the hypothesis that the highest-energy particles originate from nearby extragalactic sources whose flux has not been substantially reduced by interaction with the cosmic background radiation. AGN or objects having a similar spatial distribution are possible sources.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pierre Auger Collaboration -- Abraham, J -- Abreu, P -- Aglietta, M -- Aguirre, C -- Allard, D -- Allekotte, I -- Allen, J -- Allison, P -- Alvarez, C -- Alvarez-Muniz, J -- Ambrosio, M -- Anchordoqui, L -- Andringa, S -- Anzalone, A -- Aramo, C -- Argiro, S -- Arisaka, K -- Armengaud, E -- Arneodo, F -- Arqueros, F -- Asch, T -- Asorey, H -- Assis, P -- Atulugama, B S -- Aublin, J -- Ave, M -- Avila, G -- Backer, T -- Badagnani, D -- Barbosa, A F -- Barnhill, D -- Barroso, S L C -- Bauleo, P -- Beatty, J -- Beau, T -- Becker, B R -- Becker, K H -- Bellido, J A -- Benzvi, S -- Berat, C -- Bergmann, T -- Bernardini, P -- Bertou, X -- Biermann, P L -- Billoir, P -- Blanch-Bigas, O -- Blanco, F -- Blasi, P -- Bleve, C -- Blumer, H -- Bohacova, M -- Bonifazi, C -- Bonino, R -- Boratav, M -- Brack, J -- Brogueira, P -- Brown, W C -- Buchholz, P -- Bueno, A -- Busca, N G -- Caballero-Mora, K S -- Cai, B -- Camin, D V -- Caruso, R -- Carvalho, W -- Castellina, A -- Catalano, O -- Cataldi, G -- Cazon-Boado, L -- Cester, R -- Chauvin, J -- Chiavassa, A -- Chinellato, J A -- Chou, A -- Chye, J -- Clark, P D J -- Clay, R W -- Colombo, E -- Conceicao, R -- Connolly, B -- Contreras, F -- Coppens, J -- Cordier, A -- Cotti, U -- Coutu, S -- Covault, C E -- Creusot, A -- Cronin, J -- Dagoret-Campagne, S -- Daumiller, K -- Dawson, B R -- de Almeida, R M -- De Donato, C -- de Jong, S J -- De La Vega, G -- de Mello Junior, W J M -- de Mello Neto, J R T -- De Mitri, I -- de Souza, V -- Del Peral, L -- Deligny, O -- Selva, A Della -- Fratte, C Delle -- Dembinski, H -- Di Giulio, C -- Diaz, J C -- Dobrigkeit, C -- D'Olivo, J C -- Dornic, D -- Dorofeev, A -- Dos Anjos, J C -- Dova, M T -- D'Urso, D -- Duvernois, M A -- Engel, R -- Epele, L -- Erdmann, M -- Escobar, C O -- Etchegoyen, A -- Facal San Luis, P -- Falcke, H -- Farrar, G -- Fauth, A C -- Fazzini, N -- Fernandez, A -- Ferrer, F -- Ferry, S -- Fick, B -- Filevich, A -- Filipcic, A -- Fleck, I -- Fonte, R -- Fracchiolla, C E -- Fulgione, W -- Garcia, B -- Garcia Gamez, D -- Garcia-Pinto, D -- Garrido, X -- Geenen, H -- Gelmini, G -- Gemmeke, H -- Ghia, P L -- Giller, M -- Glass, H -- Gold, M S -- Golup, G -- Albarracin, F Gomez -- Berisso, M Gomez -- Herrero, R Gomez -- Goncalves, P -- Goncalves do Amaral, M -- Gonzalez, D -- Gonzalez, J G -- Gonzalez, M -- Gora, D -- Gorgi, A -- Gouffon, P -- Grassi, V -- Grillo, A -- Grunfeld, C -- Guardincerri, Y -- Guarino, F -- Guedes, G P -- Gutierrez, J -- Hague, J D -- Hamilton, J C -- Hansen, P -- Harari, D -- Harmsma, S -- Harton, J L -- Haungs, A -- Hauschildt, T -- Healy, M D -- Hebbeker, T -- Heck, D -- Hojvat, C -- Holmes, V C -- Homola, P -- Horandel, J -- Horneffer, A -- Horvat, M -- Hrabovsky, M -- Huege, T -- Iarlori, M -- Insolia, A -- Ionita, F -- Italiano, A -- Kaducak, M -- Kampert, K H -- Keilhauer, B -- Kemp, E -- Kieckhafer, R M -- Klages, H O -- Kleifges, M -- Kleinfeller, J -- Knapik, R -- Knapp, J -- Koang, D-H -- Kopmann, A -- Krieger, A -- Kromer, O -- Kumpel, D -- Kunka, N -- Kusenko, A -- La Rosa, G -- Lachaud, C -- Lago, B L -- Lebrun, D -- Lebrun, P -- Lee, J -- Leigui de Oliveira, M A -- Letessier-Selvon, A -- Leuthold, M -- Lhenry-Yvon, I -- Lopez, R -- Lopez Aguera, A -- Lozano Bahilo, J -- Maccarone, M C -- Macolino, C -- Maldera, S -- Malek, M -- Mancarella, G -- Mancenido, M E -- Mandat, D -- Mantsch, P -- Mariazzi, A G -- Maris, I C -- Martello, D -- Martinez, J -- Martinez Bravo, O -- Mathes, H J -- Matthews, J -- Matthews, J A J -- Matthiae, G -- Maurizio, D -- Mazur, P O -- McCauley, T -- McEwen, M -- McNeil, R R -- Medina, M C -- Medina-Tanco, G -- Meli, A -- Melo, D -- Menichetti, E -- Menschikov, A -- Meurer, Chr -- Meyhandan, R -- Micheletti, M I -- Miele, G -- Miller, W -- Mollerach, S -- Monasor, M -- Monnier Ragaigne, D -- Montanet, F -- Morales, B -- Morello, C -- Moreno, E -- Moreno, J C -- Morris, C -- Mostafa, M -- Muller, M A -- Mussa, R -- Navarra, G -- Navarro, J L -- Navas, S -- Nellen, L -- Newman-Holmes, C -- Newton, D -- Thi, T Nguyen -- Nierstenhofer, N -- Nitz, D -- Nosek, D -- Nozka, L -- Oehlschlager, J -- Ohnuki, T -- Olinto, A -- Olmos-Gilbaja, V M -- Ortiz, M -- Ostapchenko, S -- Otero, L -- Pakk Selmi-Dei, D -- Palatka, M -- Pallotta, J -- Parente, G -- Parizot, E -- Parlati, S -- Pastor, S -- Patel, M -- Paul, T -- Pavlidou, V -- Payet, K -- Pech, M -- Pekala, J -- Pelayo, R -- Pepe, I M -- Perrone, L -- Petrera, S -- Petrinca, P -- Petrov, Y -- Ngoc, Dieppham -- Ngoc, Dongpham -- Pham Thi, T N -- Pichel, A -- Piegaia, R -- Pierog, T -- Pimenta, M -- Pinto, T -- Pirronello, V -- Pisanti, O -- Platino, M -- Pochon, J -- Porter, T A -- Privitera, P -- Prouza, M -- Quel, E J -- Rautenberg, J -- Reucroft, S -- Revenu, B -- Rezende, F A S -- Ridky, J -- Riggi, S -- Risse, M -- Riviere, C -- Rizi, V -- Roberts, M -- Robledo, C -- Rodriguez, G -- Rodriguez Frias, D -- Rodriguez Martino, J -- Rodriguez Rojo, J -- Rodriguez-Cabo, I -- Ros, G -- Rosado, J -- Roth, M -- Rouille-d'Orfeuil, B -- Roulet, E -- Rovero, A C -- Salamida, F -- Salazar, H -- Salina, G -- Sanchez, F -- Santander, M -- Santo, C E -- Santos, E M -- Sarazin, F -- Sarkar, S -- Sato, R -- Scherini, V -- Schieler, H -- Schmidt, F -- Schmidt, T -- Scholten, O -- Schovanek, P -- Schussler, F -- Sciutto, S J -- Scuderi, M -- Segreto, A -- Semikoz, D -- Settimo, M -- Shellard, R C -- Sidelnik, I -- Siffert, B B -- Sigl, G -- De Grande, N Smetniansky -- Smialkowski, A -- Smida, R -- Smith, A G K -- Smith, B E -- Snow, G R -- Sokolsky, P -- Sommers, P -- Sorokin, J -- Spinka, H -- Squartini, R -- Strazzeri, E -- Stutz, A -- Suarez, F -- Suomijarvi, T -- Supanitsky, A D -- Sutherland, M S -- Swain, J -- Szadkowski, Z -- Takahashi, J -- Tamashiro, A -- Tamburro, A -- Tascau, O -- Tcaciuc, R -- Thomas, D -- Ticona, R -- Tiffenberg, J -- Timmermans, C -- Tkaczyk, W -- Todero Peixoto, C J -- Tome, B -- Tonachini, A -- Torresi, D -- Travnicek, P -- Tripathi, A -- Tristram, G -- Tscherniakhovski, D -- Tueros, M -- Tunnicliffe, V -- Ulrich, R -- Unger, M -- Urban, M -- Valdes Galicia, J F -- Valino, I -- Valore, L -- van den Berg, A M -- van Elewyck, V -- Vazquez, R A -- Veberic, D -- Veiga, A -- Velarde, A -- Venters, T -- Verzi, V -- Videla, M -- Villasenor, L -- Vorobiov, S -- Voyvodic, L -- Wahlberg, H -- Wainberg, O -- Waldenmaier, T -- Walker, P -- Warner, D -- Watson, A A -- Westerhoff, S -- Wieczorek, G -- Wiencke, L -- Wilczynska, B -- Wilczynski, H -- Wileman, C -- Winnick, M G -- Wu, H -- Wundheiler, B -- Xu, J -- Yamamoto, T -- Younk, P -- Zas, E -- Zavrtanik, D -- Zavrtanik, M -- Zech, A -- Zepeda, A -- Ziolkowski, M -- Kegl, B -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):938-43.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991855" target="_blank"〉PubMed〈/a〉

Description: Transmembrane receptors for hormones, neurotransmitters, light, and odorants mediate their cellular effects by activating heterotrimeric guanine nucleotide-binding proteins (G proteins). Crystal structures have revealed contact surfaces between G protein subunits, but not the surfaces or molecular mechanism through which Galphabetagamma responds to activation by transmembrane receptors. Such a surface was identified from the results of testing 100 mutant alpha subunits of the retinal G protein transducin for their ability to interact with rhodopsin. Sites at which alanine substitutions impaired this interaction mapped to two distinct Galpha surfaces: a betagamma-binding surface and a putative receptor-interacting surface. On the basis of these results a mechanism for receptor-catalyzed exchange of guanosine diphosphate for guanosine triphosphate is proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Onrust, R -- Herzmark, P -- Chi, P -- Garcia, P D -- Lichtarge, O -- Kingsley, C -- Bourne, H R -- CA-54427/CA/NCI NIH HHS/ -- GM-27800/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Jan 17;275(5298):381-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-0450, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8994033" target="_blank"〉PubMed〈/a〉

Description: Nanoelectromechanical resonators have potential applications in sensing, cooling, and mechanical signal processing. An important parameter in these systems is the strength of coupling the resonator motion to charge transport through the device. We investigated the mechanical oscillations of a suspended single-walled carbon nanotube that also acts as a single-electron transistor. The coupling of the mechanical and the charge degrees of freedom is strikingly strong as well as widely tunable (the associated damping rate is approximately 3 x 10(6) Hz). In particular, the coupling is strong enough to drive the oscillations in the nonlinear regime.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lassagne, Benjamin -- Tarakanov, Yury -- Kinaret, Jari -- Garcia-Sanchez, Daniel -- Bachtold, Adrian -- New York, N.Y. -- Science. 2009 Aug 28;325(5944):1107-10. doi: 10.1126/science.1174290. Epub 2009 Jul 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre d'Investigacio en Nanociencia i Nanotecnologia (Consejo Superior de Investigaciones Cientificas-Institut Catala de Nanotecnologia), campus Universitat Autonoma de Barcelona, E-08193 Barcelona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19628818" target="_blank"〉PubMed〈/a〉

Description: A major challenge in quantum optics and quantum information technology is to enhance the interaction between single photons and single quantum emitters. This requires highly engineered optical cavities that are inherently sensitive to fabrication imperfections. We have demonstrated a fundamentally different approach in which disorder is used as a resource rather than a nuisance. We generated strongly confined Anderson-localized cavity modes by deliberately adding disorder to photonic crystal waveguides. The emission rate of a semiconductor quantum dot embedded in the waveguide was enhanced by a factor of 15 on resonance with the Anderson-localized mode, and 94% of the emitted single photons coupled to the mode. Disordered photonic media thus provide an efficient platform for quantum electrodynamics, offering an approach to inherently disorder-robust quantum information devices.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sapienza, Luca -- Thyrrestrup, Henri -- Stobbe, Soren -- Garcia, Pedro David -- Smolka, Stephan -- Lodahl, Peter -- New York, N.Y. -- Science. 2010 Mar 12;327(5971):1352-5. doi: 10.1126/science.1185080.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DTU Fotonik, Department of Photonics Engineering, Technical University of Denmark, Orsteds Plads 343, DK-2800 Kgs. Lyngby, Denmark. lucs@fotonik.dtu.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20223981" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garcia, Diane -- Stokstad, Erik -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1226-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16946047" target="_blank"〉PubMed〈/a〉