Balaji Mani | Anna University (original) (raw)
Papers by Balaji Mani
Fems Microbiology Reviews, 2005
The helix-turn-helix (HTH) domain is a common denominator in basal and specific transcription fac... more The helix-turn-helix (HTH) domain is a common denominator in basal and specific transcription factors from the three super-kingdoms of life. At its core, the domain comprises of an open tri-helical bundle, which typically binds DNA with the 3rd helix. Drawing on the wealth of data that has accumulated over two decades since the discovery of the domain, we present an overview of the natural history of the HTH domain from the viewpoint of structural analysis and comparative genomics. In structural terms, the HTH domains have developed several elaborations on the basic 3-helical core, such as the tetra-helical bundle, the winged-helix and the ribbon-helix–helix type configurations. In functional terms, the HTH domains are present in the most prevalent transcription factors of all prokaryotic genomes and some eukaryotic genomes. They have been recruited to a wide range of functions beyond transcription regulation, which include DNA repair and replication, RNA metabolism and protein–protein interactions in diverse signaling contexts. Beyond their basic role in mediating macromolecular interactions, the HTH domains have also been incorporated into the catalytic domains of diverse enzymes. We discuss the general domain architectural themes that have arisen amongst the HTH domains as a result of their recruitment to these diverse functions. We present a natural classification, higher-order relationships and phyletic pattern analysis of all the major families of HTH domains. This reconstruction suggests that there were at least 6–11 different HTH domains in the last universal common ancestor of all life forms, which covered much of the structural diversity and part of the functional versatility of the extant representatives of this domain. In prokaryotes the total number of HTH domains per genome shows a strong power-equation type scaling with the gene number per genome. However, the HTH domains in two-component signaling pathways show a linear scaling with gene number, in contrast to the non-linear scaling of HTH domains in single-component systems and sigma factors. These observations point to distinct evolutionary forces in the emergence of different signaling systems with HTH transcription factors. The archaea and bacteria share a number of ancient families of specific HTH transcription factors. However, they do not share any orthologous HTH proteins in the basal transcription apparatus. This differential relationship of their basal and specific transcriptional machinery poses an apparent conundrum regarding the origins of their transcription apparatus.
Decision Support Systems, 1999
Organizations are taking advantage of ''data-mining'' techniques to leverage the vast amounts of ... more Organizations are taking advantage of ''data-mining'' techniques to leverage the vast amounts of data captured as they process routine transactions. Data mining is the process of discovering hidden structure or patterns in data. However, several of the pattern discovery methods in data-mining systems have the drawbacks that they discover too many obvious or irrelevant patterns and that they do not leverage to a full extent valuable prior domain knowledge that managers have. This research addresses these drawbacks by developing ways to generate interesting patterns by incorporating managers' prior knowledge in the process of searching for patterns in data. Specifically, we focus on providing methods that generate unexpected patterns with respect to managerial intuition by eliciting managers' beliefs about the domain and using these beliefs to seed the search for unexpected patterns in data. Our approach should lead to the development of decision-support systems that provide managers with more relevant patterns from data and aid in effective decision making. q 1999 Elsevier Science B.V. All rights reserved.
Journal of Climate, 2005
Analyses of streamflow, snowfall temperature, and precipitation in snow-melt dominated river basi... more Analyses of streamflow, snowfall temperature, and precipitation in snow-melt dominated river basins in the western US indicates an advance in the timing of peak spring flows over the past fifty years. Warm temperature spells in spring have occurred much earlier in recent years, which partly explains the trend in the timing of the spring peak flow. In addition, a decrease in snow water equivalent and a general increase in winter precipitation is evident for many weather stations in the western U.S. It appears that in recent decades more of the precipitation is coming as rain rather than snow. The trends are strongest at lower elevations and in the Pacific Northwest region, where winter temperatures are closer to the freezing-point; it appears that in this region in particular, modest shifts in temperature are capable of forcing large shifts in basin hydrologic response. We speculate that these trends could be potentially a manifestation of the general global warming trend in recent decades and also due to enhanced ENSO activity.
Many applications are characterized by having naturally incomplete data on customers -where data ... more Many applications are characterized by having naturally incomplete data on customers -where data on only some fixed set of local variables is gathered. However, having a more complete picture can help build better models. The naïve solution to this problem -acquiring complete data for all customers -is often impractical due to the costs of doing so. A possible alternative is to acquire complete data for "some" customers and to use this to improve the models built. The data acquisition problem is determining how many, and which, customers to acquire additional data from. In this paper we suggest using active learning based approaches for the data acquisition problem. In particular, we present initial methods for data acquisition and evaluate these methods experimentally on web usage data and UCI datasets. Results show that the methods perform well and indicate that active learning based methods for data acquisition can be a promising area for data mining research.
Journal of Biosciences, 1999
Lee's algorithm (1961) for routing always finds a minimum length path, if one exists. We dis... more Lee's algorithm (1961) for routing always finds a minimum length path, if one exists. We discuss an enhancement to an earlier maze-routing algorithm to reduce the number of zig-zag line segments in the routing path. This method would find a path between two points, if one exists, on a rectangular grid of cells. A line search method using efficient data structures has been applied that would reduce the number of line segments in the path. Blocking cells are introduced as obstacles in finding the path. All line segments are considered as horizontal and vertical only. An implementation of the method and its experimental results are reported
Several pattern discovery methods proposed in the data mining literature have the drawbacks that ... more Several pattern discovery methods proposed in the data mining literature have the drawbacks that they discover too many obvious or irrelevant patterns and that they do not leverage to a full extent valuable prior domain knowledge that decision makers have. In this paper we propose a new method of discovery that addresses these drawbacks. In particular we propose a new method of discovering unexpected patterns that takes into consideration prior background knowledge of decision makers. This prior knowledge constitutes a set of expectations or beliefs about the problem domain. Our proposed method of discovering unexpected patterns uses these beliefs to seed the search for patterns in data that contradict the beliefs. To evaluate the practicality of our approach, we applied our algorithm to consumer purchase data from a major market research company and to web logfile data tracked at an academic Web site and present our findings in the paper.
Communications of The ACM, 2003
Online social networks are increasingly being recognized as an important source of information in... more Online social networks are increasingly being recognized as an important source of information influencing the adoption and use of products and services. Viral marketing-the tactic of creating a process where interested people can market to each other-is therefore emerging as an important means to spread-the-word and stimulate the trial, adoption, and use of products and services.
ABSTRACT Gathering places have long been recognized as important in spreading a variety of desira... more ABSTRACT Gathering places have long been recognized as important in spreading a variety of desirable and undesirable items. One of the initial moves by authorities to stop the spreading of plague in London was to close bars where people gathered at the end of the day. In view of the large number of individuals now using the Internet routinely for communication, the possibility of tapping individuals' online networks to spread the word about a product has undeniable allure. Marketers have been the earliest to recognize this ...
Journal of The Textile Institute, 2008
Though synthetic fibres exhibit superior properties and performance compared to many natural fibr... more Though synthetic fibres exhibit superior properties and performance compared to many natural fibres, the latter has still strong acceptance in many applications. Unconventional natural fibres are often explored due to their eco-friendliness and availability in many regions. Such fibres are often used in the low cost composites, technical applications such as ropes and cordages. Borassus flabellifer L fibres, the extracts from the coverings of toddy palm fruits of palmyrah palm trees, represent the naturally available cellulosic fibres with various unique properties compared to other natural cellulosic fibres. The structural aspects and physical properties show good potential for this fibre in future.
Fems Microbiology Reviews, 2005
The helix-turn-helix (HTH) domain is a common denominator in basal and specific transcription fac... more The helix-turn-helix (HTH) domain is a common denominator in basal and specific transcription factors from the three super-kingdoms of life. At its core, the domain comprises of an open tri-helical bundle, which typically binds DNA with the 3rd helix. Drawing on the wealth of data that has accumulated over two decades since the discovery of the domain, we present an overview of the natural history of the HTH domain from the viewpoint of structural analysis and comparative genomics. In structural terms, the HTH domains have developed several elaborations on the basic 3-helical core, such as the tetra-helical bundle, the winged-helix and the ribbon-helix–helix type configurations. In functional terms, the HTH domains are present in the most prevalent transcription factors of all prokaryotic genomes and some eukaryotic genomes. They have been recruited to a wide range of functions beyond transcription regulation, which include DNA repair and replication, RNA metabolism and protein–protein interactions in diverse signaling contexts. Beyond their basic role in mediating macromolecular interactions, the HTH domains have also been incorporated into the catalytic domains of diverse enzymes. We discuss the general domain architectural themes that have arisen amongst the HTH domains as a result of their recruitment to these diverse functions. We present a natural classification, higher-order relationships and phyletic pattern analysis of all the major families of HTH domains. This reconstruction suggests that there were at least 6–11 different HTH domains in the last universal common ancestor of all life forms, which covered much of the structural diversity and part of the functional versatility of the extant representatives of this domain. In prokaryotes the total number of HTH domains per genome shows a strong power-equation type scaling with the gene number per genome. However, the HTH domains in two-component signaling pathways show a linear scaling with gene number, in contrast to the non-linear scaling of HTH domains in single-component systems and sigma factors. These observations point to distinct evolutionary forces in the emergence of different signaling systems with HTH transcription factors. The archaea and bacteria share a number of ancient families of specific HTH transcription factors. However, they do not share any orthologous HTH proteins in the basal transcription apparatus. This differential relationship of their basal and specific transcriptional machinery poses an apparent conundrum regarding the origins of their transcription apparatus.
Decision Support Systems, 1999
Organizations are taking advantage of ''data-mining'' techniques to leverage the vast amounts of ... more Organizations are taking advantage of ''data-mining'' techniques to leverage the vast amounts of data captured as they process routine transactions. Data mining is the process of discovering hidden structure or patterns in data. However, several of the pattern discovery methods in data-mining systems have the drawbacks that they discover too many obvious or irrelevant patterns and that they do not leverage to a full extent valuable prior domain knowledge that managers have. This research addresses these drawbacks by developing ways to generate interesting patterns by incorporating managers' prior knowledge in the process of searching for patterns in data. Specifically, we focus on providing methods that generate unexpected patterns with respect to managerial intuition by eliciting managers' beliefs about the domain and using these beliefs to seed the search for unexpected patterns in data. Our approach should lead to the development of decision-support systems that provide managers with more relevant patterns from data and aid in effective decision making. q 1999 Elsevier Science B.V. All rights reserved.
Journal of Climate, 2005
Analyses of streamflow, snowfall temperature, and precipitation in snow-melt dominated river basi... more Analyses of streamflow, snowfall temperature, and precipitation in snow-melt dominated river basins in the western US indicates an advance in the timing of peak spring flows over the past fifty years. Warm temperature spells in spring have occurred much earlier in recent years, which partly explains the trend in the timing of the spring peak flow. In addition, a decrease in snow water equivalent and a general increase in winter precipitation is evident for many weather stations in the western U.S. It appears that in recent decades more of the precipitation is coming as rain rather than snow. The trends are strongest at lower elevations and in the Pacific Northwest region, where winter temperatures are closer to the freezing-point; it appears that in this region in particular, modest shifts in temperature are capable of forcing large shifts in basin hydrologic response. We speculate that these trends could be potentially a manifestation of the general global warming trend in recent decades and also due to enhanced ENSO activity.
Many applications are characterized by having naturally incomplete data on customers -where data ... more Many applications are characterized by having naturally incomplete data on customers -where data on only some fixed set of local variables is gathered. However, having a more complete picture can help build better models. The naïve solution to this problem -acquiring complete data for all customers -is often impractical due to the costs of doing so. A possible alternative is to acquire complete data for "some" customers and to use this to improve the models built. The data acquisition problem is determining how many, and which, customers to acquire additional data from. In this paper we suggest using active learning based approaches for the data acquisition problem. In particular, we present initial methods for data acquisition and evaluate these methods experimentally on web usage data and UCI datasets. Results show that the methods perform well and indicate that active learning based methods for data acquisition can be a promising area for data mining research.
Journal of Biosciences, 1999
Lee's algorithm (1961) for routing always finds a minimum length path, if one exists. We dis... more Lee's algorithm (1961) for routing always finds a minimum length path, if one exists. We discuss an enhancement to an earlier maze-routing algorithm to reduce the number of zig-zag line segments in the routing path. This method would find a path between two points, if one exists, on a rectangular grid of cells. A line search method using efficient data structures has been applied that would reduce the number of line segments in the path. Blocking cells are introduced as obstacles in finding the path. All line segments are considered as horizontal and vertical only. An implementation of the method and its experimental results are reported
Several pattern discovery methods proposed in the data mining literature have the drawbacks that ... more Several pattern discovery methods proposed in the data mining literature have the drawbacks that they discover too many obvious or irrelevant patterns and that they do not leverage to a full extent valuable prior domain knowledge that decision makers have. In this paper we propose a new method of discovery that addresses these drawbacks. In particular we propose a new method of discovering unexpected patterns that takes into consideration prior background knowledge of decision makers. This prior knowledge constitutes a set of expectations or beliefs about the problem domain. Our proposed method of discovering unexpected patterns uses these beliefs to seed the search for patterns in data that contradict the beliefs. To evaluate the practicality of our approach, we applied our algorithm to consumer purchase data from a major market research company and to web logfile data tracked at an academic Web site and present our findings in the paper.
Communications of The ACM, 2003
Online social networks are increasingly being recognized as an important source of information in... more Online social networks are increasingly being recognized as an important source of information influencing the adoption and use of products and services. Viral marketing-the tactic of creating a process where interested people can market to each other-is therefore emerging as an important means to spread-the-word and stimulate the trial, adoption, and use of products and services.
ABSTRACT Gathering places have long been recognized as important in spreading a variety of desira... more ABSTRACT Gathering places have long been recognized as important in spreading a variety of desirable and undesirable items. One of the initial moves by authorities to stop the spreading of plague in London was to close bars where people gathered at the end of the day. In view of the large number of individuals now using the Internet routinely for communication, the possibility of tapping individuals' online networks to spread the word about a product has undeniable allure. Marketers have been the earliest to recognize this ...
Journal of The Textile Institute, 2008
Though synthetic fibres exhibit superior properties and performance compared to many natural fibr... more Though synthetic fibres exhibit superior properties and performance compared to many natural fibres, the latter has still strong acceptance in many applications. Unconventional natural fibres are often explored due to their eco-friendliness and availability in many regions. Such fibres are often used in the low cost composites, technical applications such as ropes and cordages. Borassus flabellifer L fibres, the extracts from the coverings of toddy palm fruits of palmyrah palm trees, represent the naturally available cellulosic fibres with various unique properties compared to other natural cellulosic fibres. The structural aspects and physical properties show good potential for this fibre in future.