M. Ganapathiraju, D. Weisser, Roni Rosenfeld, J. Carbonell, Raj Reddy, J. Klein-Seetharaman
{"title":"Comparative n-gram analysis of whole-genome protein sequences","authors":"M. Ganapathiraju, D. Weisser, Roni Rosenfeld, J. Carbonell, Raj Reddy, J. Klein-Seetharaman","doi":"10.3115/1289189.1289259","DOIUrl":"https://doi.org/10.3115/1289189.1289259","url":null,"abstract":"A current barrier for successful rational drug design is the lack of understanding of the structure space provided by the proteins in a cell that is determined by their sequence space. The protein sequences capable of folding to functional three-dimensional shapes of the proteins are clearly different for different organisms, since sequences obtained from human proteins often fail to form correct three-dimensional structures in bacterial organisms. In analogy to the question \"What kind of things do people say?\" we therefore need to ask the question \"What kind of amino acid sequences occur in the proteins of an organism?\" An understanding of the sequence space occupied by proteins in different organisms would have important applications for \"translation\" of proteins from the language of one organism into that of another and design of drugs that target sequences that might be unique or preferred by pathogenic organisms over those in human hosts. \u0000 \u0000Here we describe the development of a biological language modeling toolkit (BLMT) for genome-wide statistical amino acid n-gram analysis and comparison across organisms (freely accessible at www.cs.cmu.edu/~blmt). Its functions were applied to 44 different bacterial, archaeal and the human genome. Amino acid n-gram distribution was found to be characteristic of organisms, as evidenced by (1) the ability of simple Markovian unigram models to distinguish organisms, (2) the marked variation in n-gram distributions across organisms above random variation, and (3) identification of organism-specific phrases in protein sequences that are greater than an order of magnitude standard deviations away from the mean. These lines of evidence suggest that different organisms utilize different \"vocabularies\" and \"phrases\", an observation that may provide novel approaches to drug development by specifically targeting these phrases. The results suggest that further detailed analysis of n-gram statistics of protein sequences from whole genomes will likely - in analogy to word n-gram analysis - result in powerful models for prediction, topic classification and information extraction of bilogical sequences.","PeriodicalId":332944,"journal":{"name":"IEEE Personal Communications","volume":"61 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2002-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117076899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"European R&D on fourth-generation mobile and wireless IP networks [Guest Editorial]","authors":"P. Mahonen, George C. Polyzos","doi":"10.1109/MPC.2001.972160","DOIUrl":"https://doi.org/10.1109/MPC.2001.972160","url":null,"abstract":"","PeriodicalId":332944,"journal":{"name":"IEEE Personal Communications","volume":"64 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126447405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"How to build smart appliances?","authors":"A. Schmidt, Kristof Van Laerhoven","doi":"10.1109/98.944006","DOIUrl":"https://doi.org/10.1109/98.944006","url":null,"abstract":"In this article smart appliances are characterized as devices that are attentive to their environment. We introduce a terminology for situation, sensor data, context, and context-aware applications because it is important to gain a thorough understanding of these concepts to successfully build such artifacts. In the article the relation between a real-world situation and the data read by sensors is discussed; furthermore, an analysis of available sensing technology is given. Then we introduce an architecture that supports the transformation from sensor data to cues then to contexts as a foundation to make context-aware applications. The article suggests a method to build context-aware devices; the method starts from situation analysis, offers a structured way for selection of sensors, and finally suggests steps to determine recognition and abstraction methods. In the final part of the article the question of how this influences the applications is raised and the areas of user interfaces, communication, and proactive application scheduling are identified. We conclude with the description of a case study where a mobile phone was made aware of its environment using different sensors. The profile settings of the phone (ringing mode etc.) are automatically selected according to the real world situation the phone is used in.","PeriodicalId":332944,"journal":{"name":"IEEE Personal Communications","volume":"27 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120860982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A comparative evaluation of DECT, PACS, and PHS standards for wireless local loop applications","authors":"O. Momtahan, H. Hashemi","doi":"10.1109/35.920871","DOIUrl":"https://doi.org/10.1109/35.920871","url":null,"abstract":"In a comparative analysis the performance and capacity of DECT, PACS, and PHS for WLL applications have been investigated. This article reports the results of both qualitative and quantitative analysis. The qualitative evaluation consists of a detailed comparison of the parameters of each standard and their relevance in WLL applications. In the quantitative analysis detailed simulations have been performed covering diversified sets of conditions. The results of both types of analysis are presented. A major conclusion is that all three standards provide satisfactory performance for WLL applications. For low-traffic environments PACS, which can employ larger cells, performs better than the other two standards. In suburban areas where, in addition to coverage, capacity is an issue, DECT has better performance. For high-traffic-density urban areas with great capacity requirements all three standards have good performance.","PeriodicalId":332944,"journal":{"name":"IEEE Personal Communications","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125341229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Workshop on smart spaces [Guest Editorial]","authors":"K. Mills, J. Scholtz, K. Sollins","doi":"10.1109/MPC.2000.878534","DOIUrl":"https://doi.org/10.1109/MPC.2000.878534","url":null,"abstract":"","PeriodicalId":332944,"journal":{"name":"IEEE Personal Communications","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122070527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Smart spaces and environments [Guest Editorial]","authors":"B. R. Badrinath, M. Srivastava","doi":"10.1109/MPC.2000.878529","DOIUrl":"https://doi.org/10.1109/MPC.2000.878529","url":null,"abstract":"","PeriodicalId":332944,"journal":{"name":"IEEE Personal Communications","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132263592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Global System for Mobile Communications Short Message Service","authors":"G. Peersman, S. Cvetkovic, P. Griffiths, H. Spear","doi":"10.1109/98.847919","DOIUrl":"https://doi.org/10.1109/98.847919","url":null,"abstract":"This tutorial presents an overview of the Global System for Mobile Communications Short Message Service from the viewpoint of implementing new telematic services. The SMS offers the users of GSM networks the ability to exchange alphanumeric messages up to the limit of 160 characters. The tutorial is motivated by an acute absence of research publications in this field. The information gathered in the tutorial was required considering the increasing potential SMS offers for integration with existing messaging services and its ability to offer a successful replacement for the transmission control and Internet protocols as far as low-bandwidth-demanding applications are concerned. Initially, the tutorial gives an overview of the building blocks of GSM networks-the mobile station, base station, and network subsystem-and then emphasizes the SMS network and protocol architecture. The most widely used protocols for message submission are then introduced (text-based, SMS2000, ETSI 0705, TAP) and compared in terms of features provided and flexibility to handle extended alphabets or two-way messaging. Finally the tutorial outlines a summary of current and future issues for further development and research in the light of novel features for submission protocols and telematic services.","PeriodicalId":332944,"journal":{"name":"IEEE Personal Communications","volume":"59 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132457069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Bluetooth radio system","authors":"J. Haartsen","doi":"10.1109/98.824570","DOIUrl":"https://doi.org/10.1109/98.824570","url":null,"abstract":"A few years ago it was recognized that the vision of a truly low-cost, low-power radio-based cable replacement was feasible. Such a ubiquitous link would provide the basis for portable devices to communicate together in an ad hoc fashion by creating personal area networks which have similar advantages to their office environment counterpart, the local area network. Bluetooth/sup TM/ is an effort by a consortium of companies to design a royalty-free technology specification enabling this vision. This article describes the radio system behind the Bluetooth concept. Designing an ad hoc radio system for worldwide usage poses several challenges. The article describes the critical system characteristics and motivates the design choices that have been made.","PeriodicalId":332944,"journal":{"name":"IEEE Personal Communications","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130701333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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