From scimedweb from mail.com Wed Jan 7 05:50:21 2009 From: scimedweb from mail.com (scimedweb@mail.com) Date: Wed Jan 7 12:07:27 2009 Subject: [Bioforum] MDA-MB-435 cells are from melanoma, not from breast cancer (January 7, 2009). Message-ID: <0cda48e3-c2d1-4f74-953c-1de95ac7bbaa@n33g2000pri.googlegroups.com> MDA-MB-435 cells are from melanoma, not from breast cancer. by Marc Lacroix InTextoResearch, Baelen (Wallonia), Belgium in Cancer Chemotherapy and Pharmacology (2009) 63, 567. MDA-MB-435 cells are frequently used as =93breast cancer cells=94. Unfortunately, these are melanoma cells (1, 2). The melanocytic nature of MDA-MB-435 cells was first suspected following micro-array studies, where these cells were found to cluster with melanoma cells, rather than with other breast cancer cell lines (3). Afterward, MDA-MB-435 cells were found to express several genes commonly transcribed in melanocytes, such as RXRG, TYR, ACP5 and DCP, but which are not found in various commonly used breast cancer cell lines (4) Expression of melanocyte proteins tyrosinase and melan-A by MDA-MB-435 cells was also shown (5). MDA-MB-435 cells are in fact derived from the melanoma cell line M14, as shown by Rae et al. (6), on the basis of studies using karyotype, comparative genomic hybridization, and microsatellite polymorphism analyses, combined with bioinformatics analysis of gene expression and SNP data. The misidentification is likely to have occurred prior to 1982 and therefore, nearly all of the existing literature using the MDA-MB-435 cell line describes the M14 melanoma cell line, which has been far less studied under its true name. References 1) Lacroix M, Leclercq G (2004) Relevance of breast cancer cell lines as models for breast tumours: an update. Breast Cancer Res Treat 83:249-289 2) Lacroix M (2008) Persistent use of "false" cell lines. Int J Cancer 122:1-4 3) Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24:227-235 4) Ellison G, Klinowska T, Westwood RF, Docter E, French T, Fox JC (2002) Further evidence to support the melanocytic origin of MDA- MB-435. Mol Pathol 55:294-299. 5) Sellappan S, Grijalva R, Zhou X, Yang W, Eli MB, Mills GB, Yu D (2004) Lineage infidelity of MDA-MB-435 cells: expression of melanocyte proteins in a breast cancer cell line. Cancer Res 64:3479-3485 6) Rae JM, Creighton CJ, Meck JM, Haddad BR, Johnson MD (2007) MDA- MB-435 cells are derived from M14 melanoma cells--a loss for breast cancer, but a boon for melanoma research. Breast Cancer Res Treat 104:13-19 From evostar from na.icar.cnr.it Fri Jan 16 04:31:57 2009 From: evostar from na.icar.cnr.it (Evostar 2009) Date: Fri Jan 16 12:06:52 2009 Subject: [Bioforum] EvoPhD 2009 -- submission deadline extended Message-ID: <4970540D.5080507@na.icar.cnr.it> *** EvoPhD 2009 Submission Deadline Extension*** Due to numerous requests, we have decided to extend the submission deadline for EvoPhD event to: 31 Janauary 2009. **************** CALL FOR PAPERS **************** EvoPhD 2009 Fourth European Graduate Student Workshop on Evolutionary Computation T?bingen, Germany, 15-17 April 2009 This is the fourth European workshop on evolutionary computation that focuses on work of PhD students. Its main aim is to give students feedback on the current state of their thesis. This workshop provides a chance to students to present their work to a friendly audience of other students as well as experts in the field. It also provides students with contacts and professional networking opportunities, which helps them to integrate into the community. For you as a student, the aim of a submission is to get feedback on the current state of your thesis. Submissions will be evaluated by members of a high-quality committee that consists of long running members of the community with the goal to provide in-depth feedback. You are required to submit a paper that summarizes the research performed and planned as part of your dissertation. The number of participants is limited. Accepted papers will be published in a CD with ISSN 1974-4145, that will be disseminated among the participants of the event. The workshop is part of Evo*2009, which combined form Europe's premier co-located events in the field of evolutionary computing. The next event takes place in T?bingen, Germany. Featuring the latest in theoretical and applied research, the topics include recent genetic programming challenges, evolutionary and other meta-heuristic approaches for combinatorial optimization, evolutionary algorithms in the biosciences, in music and art domains, in image analysis and signal processing systems, in hardware optimisation and as applied to a range of industrial and financial optimisation problems. Evo*2009 web address: http://evostar.na.icar.cnr.it/index.html Topics include, but are not limited to, * Any topic that fits in the scope of the conferences and workshops * Bio-inspired computing, such as evolutionary computing, ant colony optimization, swarm intelligence, and neural networks * Local optimisation methods (tabu search, simulated annealing) * All flavours of evolutionary computation (genetic programming, evolution strategies, genetic algorithms, memetic algorithms, etc.) * Combinatorial optimisation with bio-inspired computing * Application of evolutionary computation to real-life problems * Hybrid architectures that include bio-inspired components * Theory on a relevant area of bio-inspired computing Submission Information The deadline for submission has been extended to 31 January 2009. The page limit is 14 A4 pages in Springer LCNS format. Submissions should be e-mailed in PDF or gzipped postscript to evophd@vanhemert.co.uk * Please read the formatting and content guidelines on the web page. * http://evostar.na.icar.cnr.it/EvoWorkshops/EvoPHD/EvoPHD.html Organising Committee Program Chairs Jano van Hemert jano@vanhemert.co.uk University of Edinburgh, UK Mario Giacobini mario.giacobini@unito.it University of Torino, Italy Cecilia Di Chio cecilia@stams.strath.ac.uk University of Strathclyde, UK Local Chair Marc Ebner marc.ebner@wsii.uni-tuebingen.de Universit?t T?bingen,Germany Publicity Chair Ivanoe De Falco ivanoe.defalco@na.icar.cnr.it ICAR, National Research Council of Italy, Italy From ivanoe.defalco from na.icar.cnr.it Fri Jan 16 06:22:14 2009 From: ivanoe.defalco from na.icar.cnr.it (Ivanoe De Falco) Date: Fri Jan 16 12:06:58 2009 Subject: [Bioforum] BADS 2009 - last call for papers Message-ID: <49706DE6.4000307@na.icar.cnr.it> (Apologies for multiples copies) BADS 2009 International Workshop on Bio-Inspired Algorithms for Distributed Systems http://bads.icar.cnr.it/ the Web site http://conf.icar.cnr.it is ready for the submission of papers. Deadline: January 31, 2009: Submission of Papers Selected papers will be invited to a special issue of the journal Future Generation Computer Systems, Elsevier. ********************** CALL FOR PAPERS ********************** BADS 2009 International Workshop on Bio-Inspired Algorithms for Distributed Systems http://bads.icar.cnr.it email: bads@icar.cnr.it Barcelona, Spain, June 19, 2009 In association with ICAC 2009 the 6th IEEE International Conference on Autonomic Computing & Communications Barcelona, Spain, June 15-19, 2009 **** IMPORTANT DATES **** January 31, 2009: Submission of Papers March 15, 2009: Notification of Acceptance/ Rejection April 06, 2009: Submission of Camera-Ready Copies June 19, 2009: Workshop Takes Place **** PUBLICATION **** The workshop proceedings will be published by ACM along with the proceedings of the other ICAC workshops, and distributed at the conference. **** JOURNAL SPECIAL ISSUE **** Selected papers will be invited to a special issue of the journal Future Generation Computer Systems, Elsevier (approved). **** SCOPE **** Currently used computer systems are characterized by an ever growing complexity and a pronounced distributed nature. While the use of centralized or hierarchical architectures and algorithms has been dominant so far, they are now becoming impractical because they have poor scalability and fault-tolerance characteristics. Decentralized architectures and algorithms, for example P2P and Grid systems, are increasingly popular, but they need new types of algorithms to be efficiently managed. Bio-inspired algorithms are proving effective, since they can solve hard parallel and distributed computational problems through the interaction of multiple agents. The behaviour of agents is often inspired by a number of biological systems, including ant colonies, bird flocking, honey bees, bacteria, and many more. The solution of a problem can emerge from the activity of "intelligent" agents that perform complex functionalities or from the interaction of a large number of very simple agents, in the so called "swarm intelligence" systems. These kinds of techniques feature fault-tolerant and self-adaptive behaviours that help to boost the autonomic nature of distributed systems. Such techniques are sometimes "evolutionary", as they can exploit genetic rules for the selection and the recombination of candidate solutions. Bio-inspired algorithms and systems are routinely applied to hard and large problems in a variety of areas. Some examples are optimization problems solved with genetic algorithms, routing strategies inspired by honey bee behaviour, resource discovery and data mining computations in Grid and P2P frameworks achieved by ant-inspired algorithms, and so on. The workshop aims to gather scientists, engineers, and practitioners to share and exchange their experiences, discuss challenges, and report state-of-the-art and in-progress research on Bio-Inspired Algorithms and Systems. **** AREAS OF INTEREST **** In this workshop we are interested in the exploitation of bio-inspired algorithms and systems to support the effective design and efficient implementation of distributed systems. The topics of interest include (but are not limited to): * Bio-inspired algorithms for parallel and distributed computing * Bio-inspired algorithms for P2P and Grid systems * Bio-inspired techniques for the construction and management of distributed systems * Parallel and distributed techniques of Swarm Intelligence: ant colonies, flock of birds, etc.. * Parallel and distributed evolutionary algorithms * High performance tools for bio-inspired algorithms and systems * Application of bio-inspired algorithms to routing, resource discovery, scheduling in parallel and distributed systems * Bio-inspired algorithms for data mining, bioinformatics, etc. **** ORGANIZING COMMITTEE **** Gianluigi Folino, ICAR-CNR, Italy, folino@icar.cnr.it Natalio Krasnogor, University of Nottingham, UK, nxk@cs.nott.ac.uk Carlo Mastroianni, ICAR-CNR, Italy, mastroianni@icar.cnr.it Franco Zambonelli, Universita' di Modena e Reggio Emilia, Italy, franco.zambonelli@unimore.it **** INTERNATIONAL PROGRAM COMMITTEE **** Ivanoe De Falco, ICAR-CNR, Italy Marios Dikaiakos, University of Cyprus Giovanna Di Marzo, University of London, UK Marco Dorigo, Universit? Libre de Bruxelles, Belgium Agostino Forestiero, ICAR-CNR, Italy Paraskevi Fragopoulou, FORTH-ICS, Greece Niloy Ganguly, Indian Institute of Technology, Kharagpur, India Yaohang Li, North Carolina A&T State University, USA Elena Marchiori, Radboud University, Netherlands Nicolas Monmarch?, Universit? de Tours, France Antonio Nebro Urbaneja, Universidad de M?laga, Spain Muaz Niazi, Foundation University of Islamabad, Pakistan Giuseppe Nicosia, Universit? di Catania, Italy Gauthier Picard, ?cole Nationale Sup?rieure des Mines de Saint?tienne, France Omer Rana, Cardiff University, UK Giandomenico Spezzano, ICAR-CNR, Italy Junichi Suzuki, University of Massachusetts, Boston, USA Ian Taylor, Cardiff University, UK Marco Tomassini, University of Lausanne, Switzerland Paolo Trunfio, Universit? della Calabria, Italy Naoki Wakamiya, Osaka University, Japan **** WEB SITE AND CONTACT E-MAIL **** http://bads.icar.cnr.it email: bads@icar.cnr.it **** SUBMISSION GUIDELINES **** The call is open to all members of the Autonomic Computing and Distributed Systems communities. Original papers, no longer than 8 two-column pages (including figures and references), are invited. Papers must be submitted through the Web site http://conf.icar.cnr.it. Please use the ACM format available at http://www.acm.org/sigs/pubs/proceed/template.html and submit your paper in PDF format. All manuscripts will be peer-reviewed and judged on merits including correctness, originality, technical strength, quality of presentation, and relevance to the conference themes. At least one author of each accepted submission must attend the workshop. From scimedweb from mail.com Tue Jan 20 04:51:11 2009 From: scimedweb from mail.com (scimedweb@mail.com) Date: Tue Jan 20 13:23:55 2009 Subject: [Bioforum] Comparative clinical and transcriptomal profiles of breast cancer between French and South Mediterranean patients show minor but significative biological differences. Message-ID: Comparative clinical and transcriptomal profiles of breast cancer between French and South Mediterranean patients show minor but significative biological differences. by Nass?ra Chalabi, Dominique J. Bernard-Gallon, Yves-Jean Bignon; Breast Med Consortium, Fabrice Kwiatkowski, Marie Agier, V?ronique Vidal, Val?rie Laplace-Chabaud, Val?rie Sylvain-Vidal, Vincent Bertholet, Fran?oise De Longueville, Marc Lacroix(*), Guy Leclercq, Jos? Remacle, Catherine Sibille, Nathalie Zammateo, Noureddine Ben Jaafar, Abdelaziz Sefiani, Karim Ouldim, Andr? M?garban?, Nadine Jalkh, Wejd?ne Mahfoudh, Wafa Troudi, Amel Ben Ammar-El Ga?ed, Lotfi, Chouchane in Cancer Genomics & Proteomics (2008) 5, 253-261 (*) current affiliation of Marc Lacroix: InTextoResearch, Baelen (Wallonia), Belgium BACKGROUND: In Western countries, breast cancer incidence and mortality are higher than in Mediterranean countries. These differences have been ascribed to environmental factors but also to late-stage diagnostic and biological specific characteristics. PATIENTS AND METHODS: Between September 2002 and September 2005, we collected clinical data by phone counselling 180 French and Mediterranean breast cancer patients and performed microarray experiments. RESULTS: Characteristics of breast cancer in patients from Lebanon, Tunisia and Morocco were more aggressive (more SBR grade III and positive node invasion) and patients were 10 years younger at diagnosis. Sixteen differentially expressed genes such as MMP9, VEGF, PHB1, BRCA1, TFAP2C, GJA1 and TFF1 were also found. Additionally, an up-regulation of cytokeratins KRT8 and KRT18 may indicate a luminal B subtype in "South" (Lebanon, Tunisia and Morocco) tumors while "North" (France) tumors may more frequently be luminal A type. CONCLUSION: This study allowed the identification of specific clinical and transcriptomic parameters in patients from South Mediterranean countries. From yzhang from CS.Trinity.Edu Thu Jan 22 18:26:18 2009 From: yzhang from CS.Trinity.Edu (Yu Zhang) Date: Thu Jan 22 19:17:52 2009 Subject: [Bioforum] IEEE SMC 2009 -- Call for Papers, Special Sessions, and Tutorials/Workshops Message-ID: ========================================================== CALL FOR PAPERS, SPECIAL SESSIONS, AND TUTORIALS/WORKSHOPS 2009 IEEE International Conference on Systems, Man, and Cybernetics (IEEE SMC 2009) Hyatt Regency Riverwalk, San Antonio, Texas, USA. October 11-14, 2009 http://www.smc2009.org ========================================================== Theme: Intelligent Human-Machine Systems for Quality of Life Prospective authors are invited to submit their full paper(s) electronically through the conference website. Each paper should be concise, but contain sufficient detail and references to allow critical review. Each paper will be judged by at least two referees. Accepted papers will appear in the conference proceedings only if one of the authors is registered for the conference and is presenting the work. The goal of Special Sessions (SS) is to provide a focused discussion of new or innovative topics. SS organizer(s) must collect at least five papers. An individual can download an SMC2009 SS proposal form from SMC2009 official site, and send a full-filled form to the SS Chair. SS papers will be reviewed with the same criteria as Regular Session papers. Please check website for submission process and other details. Important Dates Feb 1, 2009: Deadline for submission of proposals for Special Sessions. Mar 15, 2009: Deadline for submission of full-length papers for Regular Sessions and Special Sessions. Apr 15, 2009: Deadline for submission of proposals for Tutorials/Workshops May 15, 2009: Acceptance/Rejection notification for Tutorials/Workshops May 15, 2009: Acceptance/Rejection notification for regular papers and special session papers. Jun 29, 2009: Final camera-ready papers due in electronic form and deadline for submitting tutorial/workshop materials. PDF version of full Call for Papers is available from: http://www.smc2009.org/CFP.pdf ------------------------------ This Call for Papers is sent to you by the sender who believes that you might be interested in SMC 2009. We would also appreciate if you could help us forward this Call for Papers to those who might be interested. We apologize if you received multiple copies of this announcement. ------------------------------ From fatos.cenalia from gmail.com Sat Jan 24 08:49:23 2009 From: fatos.cenalia from gmail.com (Fatos Cenalia) Date: Sat Jan 24 11:41:17 2009 Subject: [Bioforum] Sodium Fluorosilicate Disposal ideas Message-ID: Dear Forum experts; I have ideas how to dispose wastes of dry (cristaline material) Sodium Fluorosilicate that I would like to discuss and share with you. The first idea is: "The neutralization proces by chemical reaction to bring back to native Apatite The second idea is: "The controlled discharge by regulated percentage of mixing with river water in high quantities" I will appreciate you comments on above. Eng. F. Cenalia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/bioforum/attachments/20090124/557d6856/attachment.html From prae from gmx.net Sat Jan 24 16:48:07 2009 From: prae from gmx.net (Christian Praetorius) Date: Sun Jan 25 12:19:40 2009 Subject: [Bioforum] Re: Sodium Fluorosilicate Disposal ideas References: Message-ID: <6u1gknFcaahfU1@mid.individual.net> Fatos Cenalia wrote: >I have ideas how to dispose wastes of dry (cristaline material) Sodium >Fluorosilicate that I would like to discuss and share with you. Contact the guy at your department who is responsible for that. And please put the stuff in your hazardous chemicals waste and nowhere else. Christian -- X-no-Sig: yes From evostar from na.icar.cnr.it Tue Jan 27 09:38:16 2009 From: evostar from na.icar.cnr.it (Evostar 2009) Date: Tue Jan 27 12:43:49 2009 Subject: [Bioforum] EvoPhD 2009 -- submission deadline extended -- last reminder Message-ID: <497F1C58.9080003@na.icar.cnr.it> *** EvoPhD 2009 Submission Deadline Extension*** Due to numerous requests, we have decided to extend the submission deadline for EvoPhD event to: 31 January 2009. **************** CALL FOR PAPERS **************** EvoPhD 2009 Fourth European Graduate Student Workshop on Evolutionary Computation T?bingen, Germany, 15-17 April 2009 This is the fourth European workshop on evolutionary computation that focuses on work of PhD students. Its main aim is to give students feedback on the current state of their thesis. This workshop provides a chance to students to present their work to a friendly audience of other students as well as experts in the field. It also provides students with contacts and professional networking opportunities, which helps them to integrate into the community. For you as a student, the aim of a submission is to get feedback on the current state of your thesis. Submissions will be evaluated by members of a high-quality committee that consists of long running members of the community with the goal to provide in-depth feedback. You are required to submit a paper that summarizes the research performed and planned as part of your dissertation. The number of participants is limited. Accepted papers will be published in a CD with ISSN 1974-4145, that will be disseminated among the participants of the event. The workshop is part of Evo*2009, which combined form Europe's premier co-located events in the field of evolutionary computing. The next event takes place in T?bingen, Germany. Featuring the latest in theoretical and applied research, the topics include recent genetic programming challenges, evolutionary and other meta-heuristic approaches for combinatorial optimization, evolutionary algorithms in the biosciences, in music and art domains, in image analysis and signal processing systems, in hardware optimisation and as applied to a range of industrial and financial optimisation problems. Evo*2009 web address: http://evostar.na.icar.cnr.it/index.html Topics include, but are not limited to, * Any topic that fits in the scope of the conferences and workshops * Bio-inspired computing, such as evolutionary computing, ant colony optimization, swarm intelligence, and neural networks * Local optimisation methods (tabu search, simulated annealing) * All flavours of evolutionary computation (genetic programming, evolution strategies, genetic algorithms, memetic algorithms, etc.) * Combinatorial optimisation with bio-inspired computing * Application of evolutionary computation to real-life problems * Hybrid architectures that include bio-inspired components * Theory on a relevant area of bio-inspired computing Submission Information The deadline for submission has been extended to 31 January 2009. The page limit is 14 A4 pages in Springer LCNS format. Submissions should be e-mailed in PDF or gzipped postscript to evophd@vanhemert.co.uk * Please read the formatting and content guidelines on the web page. * http://evostar.na.icar.cnr.it/EvoWorkshops/EvoPHD/EvoPHD.html Organising Committee Program Chairs Jano van Hemert jano@vanhemert.co.uk University of Edinburgh, UK Mario Giacobini mario.giacobini@unito.it University of Torino, Italy Cecilia Di Chio cecilia@stams.strath.ac.uk University of Strathclyde, UK Local Chair Marc Ebner marc.ebner@wsii.uni-tuebingen.de Universit?t T?bingen,Germany Publicity Chair Ivanoe De Falco ivanoe.defalco@na.icar.cnr.it ICAR, National Research Council of Italy, Italy From yzhang from CS.Trinity.Edu Mon Jan 26 18:04:48 2009 From: yzhang from CS.Trinity.Edu (Yu Zhang) Date: Tue Jan 27 12:55:14 2009 Subject: [Bioforum] Call for Papers and Special Sessions, 2009 Summer Computer SimulationConference, July 13-16, 2009, Istanbul, Turkey Message-ID: ================================================================== 2009 Summer Computer Simulation Conference (SCSC'09) Grand Cevahir Hotel and Convention Center Istanbul, Turkey July 13-16, 2009 http://www.eng.auburn.edu/~yilmaz/SCSC09-CFP.htm Sponsored by The Society for Modeling and Simulation International ================================================================== As part of the 2009 International Simulation Multi-conference (ISMc'09) http://www.scs.org/confernc/summersim/summersim09/cfp/summersim09.htm , the 2009 Summer Computer Simulation Conference (SCSC'09) is a premier international forum and annual conference sponsored by The Society for Modeling and Simulation International which covers state-of-the-art developments in computer simulation methodologies, technologies, as well as scientific, industrial, and business applications. SCSC'09 features a comprehensive program ranging from introductory tutorials to state of the art research and practice. SCSC'09 includes keynote speeches presented by technology and industry leaders, technical sessions, professional development courses and seminars, poster presentations; as well as vendor exhibits. Papers and proposals for panels, tutorials, workshops, seminars, exhibits, other technical are solicited. All contributed papers will be peer reviewed. Papers should be submitted electronically to http://www.softconf.com/scs/SCSC09/. Final version of all the papers should comply with the SCS conference format. The best contributed paper will be given an award sponsored by ACM SIGSIM. A selected group of full papers will be published in the special issue of the Simulation Journal. Please note the following deadlines: Jan 31, 2009: Special session proposals Feb 25, 2009: Submission of papers Apr 21, 2009: Notification of Acceptance May 15, 2009: Final Submission The list of topics is avaliable from the confernce website: http://www.eng.auburn.edu/~yilmaz/SCSC09-CFP.htm General Chair Levent Yilmaz, Auburn University, USA Program Chairs Osman Balci, Virginia Tech, USA Xiaolin Hu, Georgia State University, USA Maarten Sierhuis, NASA, USA Current List of Workshops: Agent-directed Simulation Chairs: Tuncer ?ren, SITE, University of Ottawa (Canada); Levent Yilmaz, Auburn University (USA). Applications in Business, Management, Planning & Logistics Chair: Agostino Bruzzone, University of Genoa (Italy). Bioinformatics / Biology Chair: Isaac Barjis, New York City College of Technology (USA). Computer Graphics for Simulation Chair: John F. Richardson, SPAWAR Systems Center, PACIFIC (USA) Emergency Simulation Chair: Francesco Longo, University of Calabria (Italy) Engineering and Management in the M&S Discipline Chairs: Andreas Tolk, Old Dominion University (USA); Resit Unal, Old Dominion University (USA). Rich Cognitive Models for Policy design and Simulation Chair: Virginia Dignum, University of Utrecht (Netherlands).