David A Liberles (ed.)
- Published in print:
- 2007
- Published Online:
- September 2008
- ISBN:
- 9780199299188
- eISBN:
- 9780191714979
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199299188.001.0001
- Subject:
- Biology, Evolutionary Biology / Genetics
Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological ...
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Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in almost all fields of applied molecular biology. This book starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including whole proteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a description of the scientific questions where experimental ancestral sequence reconstruction has been utilized to provide insights and inform future research.Less
Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in almost all fields of applied molecular biology. This book starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including whole proteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a description of the scientific questions where experimental ancestral sequence reconstruction has been utilized to provide insights and inform future research.
Roger W. Shuy
- Published in print:
- 2008
- Published Online:
- May 2008
- ISBN:
- 9780195328837
- eISBN:
- 9780199870165
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195328837.003.0009
- Subject:
- Linguistics, Sociolinguistics / Anthropological Linguistics
This product liability case brought against a company that produced a ship cleaning product centered on the warning label for the cleaning product, which had caused a worker's brain damage. ...
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This product liability case brought against a company that produced a ship cleaning product centered on the warning label for the cleaning product, which had caused a worker's brain damage. Comparison was made between the industry safety standards for the precautionary labeling of industrial chemicals and the text on the cleaning product's container. The wording of the warning section on the container was not prominent to the potential danger of the product. The communication of the dangers that users might encounter were unclear, and the advice about what to do if users got into trouble using it were not conveyed explicitly. The discourse sequencing within the warnings placed the least crucial information before the most crucial and provided no information about what to do to avoid the hazards that the product contained. The plaintiff also rewrote the text of the container to show how it could have been user-friendly and to communicate useful information and prevent further harm.Less
This product liability case brought against a company that produced a ship cleaning product centered on the warning label for the cleaning product, which had caused a worker's brain damage. Comparison was made between the industry safety standards for the precautionary labeling of industrial chemicals and the text on the cleaning product's container. The wording of the warning section on the container was not prominent to the potential danger of the product. The communication of the dangers that users might encounter were unclear, and the advice about what to do if users got into trouble using it were not conveyed explicitly. The discourse sequencing within the warnings placed the least crucial information before the most crucial and provided no information about what to do to avoid the hazards that the product contained. The plaintiff also rewrote the text of the container to show how it could have been user-friendly and to communicate useful information and prevent further harm.
Tom W. N. Parker
- Published in print:
- 1998
- Published Online:
- October 2011
- ISBN:
- 9780198184430
- eISBN:
- 9780191674259
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198184430.003.0008
- Subject:
- Literature, Poetry, 16th-century and Renaissance Literature
This conclusion concludes that the frequency in the reiterations of particular sets of numbers within the sonnet sequences of the Sidney circle is an enough conviction that intentional patterning did ...
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This conclusion concludes that the frequency in the reiterations of particular sets of numbers within the sonnet sequences of the Sidney circle is an enough conviction that intentional patterning did existed. The Renaissance was a period governed by appreciation of harmony and aesthetic considerations, hence sonnet sequence within a harmonic pattern were deeply appreciated. In the works of Fulke Greville, Robert Sidney and Phillip Sidney, the recurrence of the same set of numbers in the formal arrangements of the sonnet sequences implied the purpose and implication of harmonic sequences — intentional patterning and formal sonnet sequences were indications of the technicalities that sought to belie the perceived shallowness of sonnets and poetry. While fastidious attention is directed to the superficial and surface features of poems, the formal sonnet sequences allows if not forces a reader to look beyond the superficiality of poetry to the sweat and blood invested by the poets to the algorithms and sequences of their craft.Less
This conclusion concludes that the frequency in the reiterations of particular sets of numbers within the sonnet sequences of the Sidney circle is an enough conviction that intentional patterning did existed. The Renaissance was a period governed by appreciation of harmony and aesthetic considerations, hence sonnet sequence within a harmonic pattern were deeply appreciated. In the works of Fulke Greville, Robert Sidney and Phillip Sidney, the recurrence of the same set of numbers in the formal arrangements of the sonnet sequences implied the purpose and implication of harmonic sequences — intentional patterning and formal sonnet sequences were indications of the technicalities that sought to belie the perceived shallowness of sonnets and poetry. While fastidious attention is directed to the superficial and surface features of poems, the formal sonnet sequences allows if not forces a reader to look beyond the superficiality of poetry to the sweat and blood invested by the poets to the algorithms and sequences of their craft.
J. R. Hicks
- Published in print:
- 1987
- Published Online:
- November 2003
- ISBN:
- 9780198772866
- eISBN:
- 9780191596414
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/0198772866.001.0001
- Subject:
- Economics and Finance, Macro- and Monetary Economics
This book, first published in 1973, takes up an important approach to capital which had gone out of fashion. There has been some recent renewed interest in this approach. The ‘Austrian’ theory of ...
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This book, first published in 1973, takes up an important approach to capital which had gone out of fashion. There has been some recent renewed interest in this approach. The ‘Austrian’ theory of capital concentrates on the inputs and outputs in the productive process, and has an advantage over more modern theories of economic dynamics in that it is more naturally expressible in economic terms: the production process over time is taken as a whole, rather than disintegrated. However, this approach had been largely abandoned because it seemed to be unable to deal with fixed capital. The book overcomes this problem here by allowing for a sequence of outputs, and the consequences for dynamic economics are profound and novel.Less
This book, first published in 1973, takes up an important approach to capital which had gone out of fashion. There has been some recent renewed interest in this approach. The ‘Austrian’ theory of capital concentrates on the inputs and outputs in the productive process, and has an advantage over more modern theories of economic dynamics in that it is more naturally expressible in economic terms: the production process over time is taken as a whole, rather than disintegrated. However, this approach had been largely abandoned because it seemed to be unable to deal with fixed capital. The book overcomes this problem here by allowing for a sequence of outputs, and the consequences for dynamic economics are profound and novel.
Tom W. N. Parker
- Published in print:
- 1998
- Published Online:
- October 2011
- ISBN:
- 9780198184430
- eISBN:
- 9780191674259
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198184430.001.0001
- Subject:
- Literature, Poetry, 16th-century and Renaissance Literature
The structure of Philip Sidney's Astrophil and Stella is governed by a distinctive and complex set of proportions, found also in the sonnet sequences of Fulke Greville and Robert Sidney written under ...
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The structure of Philip Sidney's Astrophil and Stella is governed by a distinctive and complex set of proportions, found also in the sonnet sequences of Fulke Greville and Robert Sidney written under its influence. For all these works to be ordered around the same set of proportions indicates a remarkable degree of careful planning and precise execution, and in turn affects their meaning. The tremendous effort of constructing the sequences according to intricate mathematical patterns suggests that the patterns themselves held a particular significance, one that requires investigation for the light it throws on these authors' intentions in composition. This study reveals cosmological ideas implicit in the form of Astrophil and Stella, ideas which not only undermine much of the romantic and biographically-based criticism of the sequence, but call into question how we should read the sonnet sequences that were influenced by Sidney, both within and beyond his immediate circle. As well as those of Greville and Robert Sidney, the book looks in detail at the sonnet sequences of Giordano Bruno, Mary Wroth, Henry Constable, Barnabe Barnes, and Michael Drayton, to determine the extent to which the sonnet vogue of the 1590s incorporated Sidney's broader cosmological concerns.Less
The structure of Philip Sidney's Astrophil and Stella is governed by a distinctive and complex set of proportions, found also in the sonnet sequences of Fulke Greville and Robert Sidney written under its influence. For all these works to be ordered around the same set of proportions indicates a remarkable degree of careful planning and precise execution, and in turn affects their meaning. The tremendous effort of constructing the sequences according to intricate mathematical patterns suggests that the patterns themselves held a particular significance, one that requires investigation for the light it throws on these authors' intentions in composition. This study reveals cosmological ideas implicit in the form of Astrophil and Stella, ideas which not only undermine much of the romantic and biographically-based criticism of the sequence, but call into question how we should read the sonnet sequences that were influenced by Sidney, both within and beyond his immediate circle. As well as those of Greville and Robert Sidney, the book looks in detail at the sonnet sequences of Giordano Bruno, Mary Wroth, Henry Constable, Barnabe Barnes, and Michael Drayton, to determine the extent to which the sonnet vogue of the 1590s incorporated Sidney's broader cosmological concerns.
Ziheng Yang
- Published in print:
- 2006
- Published Online:
- April 2010
- ISBN:
- 9780198567028
- eISBN:
- 9780191728280
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198567028.001.0001
- Subject:
- Biology, Evolutionary Biology / Genetics
The field of molecular evolution has experienced explosive growth in recent years due to the rapid accumulation of genetic sequence data, continuous improvements to computer hardware and software, ...
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The field of molecular evolution has experienced explosive growth in recent years due to the rapid accumulation of genetic sequence data, continuous improvements to computer hardware and software, and the development of sophisticated analytical methods. The increasing availability of large genomic data sets requires powerful statistical methods to analyse and interpret them, generating both computational and conceptual challenges for the field. This book provides a comprehensive coverage of modern statistical and computational methods used in molecular evolutionary analysis, such as maximum likelihood and Bayesian statistics. It describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes. The book emphasizes essential concepts rather than mathematical proofs. It includes detailed derivations and implementation details, as well as numerous illustrations, worked examples, and exercises.Less
The field of molecular evolution has experienced explosive growth in recent years due to the rapid accumulation of genetic sequence data, continuous improvements to computer hardware and software, and the development of sophisticated analytical methods. The increasing availability of large genomic data sets requires powerful statistical methods to analyse and interpret them, generating both computational and conceptual challenges for the field. This book provides a comprehensive coverage of modern statistical and computational methods used in molecular evolutionary analysis, such as maximum likelihood and Bayesian statistics. It describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes. The book emphasizes essential concepts rather than mathematical proofs. It includes detailed derivations and implementation details, as well as numerous illustrations, worked examples, and exercises.
Mark D. LeBlanc and Betsey Dexter Dyer
- Published in print:
- 2007
- Published Online:
- April 2010
- ISBN:
- 9780195305890
- eISBN:
- 9780199773862
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195305890.003.15
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies
Anton van Leeuwenhoek, the microscopist, was in great demand as a party guest in fashionable Delft homes in the 17th century. He could be counted upon to bring along several hand-held microscopes ...
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Anton van Leeuwenhoek, the microscopist, was in great demand as a party guest in fashionable Delft homes in the 17th century. He could be counted upon to bring along several hand-held microscopes with glass bead lenses on which he would mount diverse specimens, including scrapings from between the teeth of his fellow guests. Often we simply do not see what we do not (yet) understand. The problem in sequence analysis is compounded by the sheer quantity of the unanalyzed information and the indirect methods by which that information is deciphered. How much information is slipping through our current methods of classification and decoding, because we do not yet have the context by which to design the right search tools? Industrial labs, academic labs, granting agencies, and editors of journals often have clear visions and definitive opinions of what sorts of sequences are worth collecting, analyzing, and using; traditionally, gene sequences have been featured high on their lists. Indeed the annotation of any new genome begins and often ends with a catalogue of which genes are present. Often the sequences between genes are ignored. When such intergenic sequences are analyzed, they do not become neatly classified and organized into pre-existing databases, designed with genes in mind. Meaningful information, which often reveals itself in well-organized datasets, may not be visible at all.Less
Anton van Leeuwenhoek, the microscopist, was in great demand as a party guest in fashionable Delft homes in the 17th century. He could be counted upon to bring along several hand-held microscopes with glass bead lenses on which he would mount diverse specimens, including scrapings from between the teeth of his fellow guests. Often we simply do not see what we do not (yet) understand. The problem in sequence analysis is compounded by the sheer quantity of the unanalyzed information and the indirect methods by which that information is deciphered. How much information is slipping through our current methods of classification and decoding, because we do not yet have the context by which to design the right search tools? Industrial labs, academic labs, granting agencies, and editors of journals often have clear visions and definitive opinions of what sorts of sequences are worth collecting, analyzing, and using; traditionally, gene sequences have been featured high on their lists. Indeed the annotation of any new genome begins and often ends with a catalogue of which genes are present. Often the sequences between genes are ignored. When such intergenic sequences are analyzed, they do not become neatly classified and organized into pre-existing databases, designed with genes in mind. Meaningful information, which often reveals itself in well-organized datasets, may not be visible at all.
Duana Fullwiley
- Published in print:
- 2011
- Published Online:
- October 2017
- ISBN:
- 9780691123165
- eISBN:
- 9781400840410
- Item type:
- book
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691123165.001.0001
- Subject:
- Anthropology, Social and Cultural Anthropology
In the 1980s, a research team led by Parisian scientists identified several unique DNA sequences, or haplotypes, linked to sickle cell anemia in African populations. After casual observations of how ...
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In the 1980s, a research team led by Parisian scientists identified several unique DNA sequences, or haplotypes, linked to sickle cell anemia in African populations. After casual observations of how patients managed this painful blood disorder, the researchers in question postulated that the Senegalese type was less severe. This book traces how this genetic discourse has blotted from view the roles that Senegalese patients and doctors have played in making sickle cell “mild” in a social setting where public health priorities and economic austerity programs have forced people to improvise informal strategies of care. The book shows how geneticists, who were fixated on population differences, never investigated the various modalities of self-care that people developed in this context of biomedical scarcity, and how local doctors, confronted with dire cuts in Senegal's health sector, wittingly accepted the genetic prognosis of better-than-expected health outcomes. Unlike most genetic determinisms that highlight the absoluteness of disease, DNA haplotypes for sickle cell in Senegal did the opposite. As the book demonstrates, they allowed the condition to remain officially invisible, never to materialize as a health priority. At the same time, scientists' attribution of a less severe form of Senegalese sickle cell to isolated DNA sequences closed off other explanations of this population's measured biological success. This book reveals how the notion of an advantageous form of sickle cell in this part of West Africa has defined—and obscured—the nature of this illness in Senegal today.Less
In the 1980s, a research team led by Parisian scientists identified several unique DNA sequences, or haplotypes, linked to sickle cell anemia in African populations. After casual observations of how patients managed this painful blood disorder, the researchers in question postulated that the Senegalese type was less severe. This book traces how this genetic discourse has blotted from view the roles that Senegalese patients and doctors have played in making sickle cell “mild” in a social setting where public health priorities and economic austerity programs have forced people to improvise informal strategies of care. The book shows how geneticists, who were fixated on population differences, never investigated the various modalities of self-care that people developed in this context of biomedical scarcity, and how local doctors, confronted with dire cuts in Senegal's health sector, wittingly accepted the genetic prognosis of better-than-expected health outcomes. Unlike most genetic determinisms that highlight the absoluteness of disease, DNA haplotypes for sickle cell in Senegal did the opposite. As the book demonstrates, they allowed the condition to remain officially invisible, never to materialize as a health priority. At the same time, scientists' attribution of a less severe form of Senegalese sickle cell to isolated DNA sequences closed off other explanations of this population's measured biological success. This book reveals how the notion of an advantageous form of sickle cell in this part of West Africa has defined—and obscured—the nature of this illness in Senegal today.
Joseph E. Stiglitz, José Antonio Ocampo, Shari Spiegel, Ricardo Ffrench-Davis, and Deepak Nayyar
- Published in print:
- 2006
- Published Online:
- September 2006
- ISBN:
- 9780199288144
- eISBN:
- 9780191603884
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/0199288143.003.0013
- Subject:
- Economics and Finance, Development, Growth, and Environmental
This chapter examines some of the other outstanding debates on capital market liberalization (CML). In particular, it focuses on when a country is sufficiently developed to risk capital market ...
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This chapter examines some of the other outstanding debates on capital market liberalization (CML). In particular, it focuses on when a country is sufficiently developed to risk capital market liberalization, whether all countries should make liberalization their long-term goal, and whether capital market liberalization is reversible; even if it was a mistake in the first place, should countries that have already liberalized now stick with it? For example, proponents of liberalization often argue that the issue is not whether countries should liberalize their capital markets, but rather that liberalization should occur within the ‘proper’ sequence of reforms. Critics, however, argue that CML should not necessarily be the long run goal of all countries and that there are better ways for developing countries to integrate into the global economy. The chapter also contains a section that examines the appropriateness of different techniques of capital market liberalization for countries in various stages of development.Less
This chapter examines some of the other outstanding debates on capital market liberalization (CML). In particular, it focuses on when a country is sufficiently developed to risk capital market liberalization, whether all countries should make liberalization their long-term goal, and whether capital market liberalization is reversible; even if it was a mistake in the first place, should countries that have already liberalized now stick with it? For example, proponents of liberalization often argue that the issue is not whether countries should liberalize their capital markets, but rather that liberalization should occur within the ‘proper’ sequence of reforms. Critics, however, argue that CML should not necessarily be the long run goal of all countries and that there are better ways for developing countries to integrate into the global economy. The chapter also contains a section that examines the appropriateness of different techniques of capital market liberalization for countries in various stages of development.
Leigh Marie Braswell and Tanya Khovanova
- Published in print:
- 2015
- Published Online:
- October 2017
- ISBN:
- 9780691164038
- eISBN:
- 9781400881338
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691164038.003.0016
- Subject:
- Mathematics, History of Mathematics
This chapter examines the problem of the “Cookie Monster number.” In 2002, Cookie Monster® appeared in the book The Inquisitive Problem Solver by Vaderlind, Guy, and Larson, where the hungry monster ...
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This chapter examines the problem of the “Cookie Monster number.” In 2002, Cookie Monster® appeared in the book The Inquisitive Problem Solver by Vaderlind, Guy, and Larson, where the hungry monster wants to empty a set of jars filled with various numbers of cookies. The Cookie Monster number is the minimum number of moves Cookie Monster must use to empty all the jars. The chapter analyzes this problem by first introducing known general algorithms and known bounds for the Cookie Monster number. It then explicitly finds the Cookie Monster number for jars containing cookies in the Fibonacci, Tribonacci, n-nacci, and Super-n-nacci sequences. The chapter also constructs sequences of k jars such that their Cookie Monster numbers are asymptotically rk, where r is any real number, 0 ≤ r ≤ 1.Less
This chapter examines the problem of the “Cookie Monster number.” In 2002, Cookie Monster® appeared in the book The Inquisitive Problem Solver by Vaderlind, Guy, and Larson, where the hungry monster wants to empty a set of jars filled with various numbers of cookies. The Cookie Monster number is the minimum number of moves Cookie Monster must use to empty all the jars. The chapter analyzes this problem by first introducing known general algorithms and known bounds for the Cookie Monster number. It then explicitly finds the Cookie Monster number for jars containing cookies in the Fibonacci, Tribonacci, n-nacci, and Super-n-nacci sequences. The chapter also constructs sequences of k jars such that their Cookie Monster numbers are asymptotically rk, where r is any real number, 0 ≤ r ≤ 1.
D. Huybrechts
- Published in print:
- 2006
- Published Online:
- September 2007
- ISBN:
- 9780199296866
- eISBN:
- 9780191711329
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199296866.003.0002
- Subject:
- Mathematics, Geometry / Topology
This chapter briefly outlines the main steps in the construction of the derived category of an arbitrary abelian category. The homotopy category of complexes is considered as an intermediate step, ...
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This chapter briefly outlines the main steps in the construction of the derived category of an arbitrary abelian category. The homotopy category of complexes is considered as an intermediate step, which is then localized with respect to quasi-isomorphisms. Left and right derived functors are explained in general, and particular examples are studied in more detail. Spectral sequences are treated in a separate section.Less
This chapter briefly outlines the main steps in the construction of the derived category of an arbitrary abelian category. The homotopy category of complexes is considered as an intermediate step, which is then localized with respect to quasi-isomorphisms. Left and right derived functors are explained in general, and particular examples are studied in more detail. Spectral sequences are treated in a separate section.
D. Huybrechts
- Published in print:
- 2006
- Published Online:
- September 2007
- ISBN:
- 9780199296866
- eISBN:
- 9780191711329
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199296866.003.0004
- Subject:
- Mathematics, Geometry / Topology
This chapter is devoted to results by Bondal and Orlov which show that for varieties with ample (anti-)canonical bundle, the bounded derived category of coherent sheaves determines the variety. ...
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This chapter is devoted to results by Bondal and Orlov which show that for varieties with ample (anti-)canonical bundle, the bounded derived category of coherent sheaves determines the variety. Except for the case of elliptic curves, this settles completely the classification of derived categories of smooth curves. The complexity of the derived category is reflected by its group of autoequivalences. This is studied by means of ample sequences.Less
This chapter is devoted to results by Bondal and Orlov which show that for varieties with ample (anti-)canonical bundle, the bounded derived category of coherent sheaves determines the variety. Except for the case of elliptic curves, this settles completely the classification of derived categories of smooth curves. The complexity of the derived category is reflected by its group of autoequivalences. This is studied by means of ample sequences.
D. Huybrechts
- Published in print:
- 2006
- Published Online:
- September 2007
- ISBN:
- 9780199296866
- eISBN:
- 9780191711329
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199296866.003.0008
- Subject:
- Mathematics, Geometry / Topology
Spherical objects — motivated by considerations in the context of mirror symmetry — are used to construct special autoequivalences. Their action on cohomology can be described precisely, considering ...
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Spherical objects — motivated by considerations in the context of mirror symmetry — are used to construct special autoequivalences. Their action on cohomology can be described precisely, considering more than one spherical object often leads to complicated (braid) groups acting on the derived category. The results related to Beilinson are almost classical. Section 3 of this chapter gives an account of the Beilinson spectral sequence and how it is used to deduce a complete description of the derived category of the projective space. This will use the language of exceptional sequences and semi-orthogonal decompositions encountered here. The final section gives a simplified account of the work of Horja, which extends the theory of spherical objects and their associated twists to a broader geometric context.Less
Spherical objects — motivated by considerations in the context of mirror symmetry — are used to construct special autoequivalences. Their action on cohomology can be described precisely, considering more than one spherical object often leads to complicated (braid) groups acting on the derived category. The results related to Beilinson are almost classical. Section 3 of this chapter gives an account of the Beilinson spectral sequence and how it is used to deduce a complete description of the derived category of the projective space. This will use the language of exceptional sequences and semi-orthogonal decompositions encountered here. The final section gives a simplified account of the work of Horja, which extends the theory of spherical objects and their associated twists to a broader geometric context.
Rein Taagepera
- Published in print:
- 2008
- Published Online:
- September 2008
- ISBN:
- 9780199534661
- eISBN:
- 9780191715921
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199534661.003.0010
- Subject:
- Political Science, Comparative Politics, Political Economy
Interlocking networks of equations, based on logical models, are possible in social sciences. Partial evidence is offered by a sequence of models that ties mean duration of governmental cabinets ...
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Interlocking networks of equations, based on logical models, are possible in social sciences. Partial evidence is offered by a sequence of models that ties mean duration of governmental cabinets first to the number of parties and then to the number of seats in the electoral district and the entire representative assembly.Less
Interlocking networks of equations, based on logical models, are possible in social sciences. Partial evidence is offered by a sequence of models that ties mean duration of governmental cabinets first to the number of parties and then to the number of seats in the electoral district and the entire representative assembly.
F. Nicholas Braun
- Published in print:
- 2007
- Published Online:
- September 2008
- ISBN:
- 9780199299188
- eISBN:
- 9780191714979
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199299188.003.0007
- Subject:
- Biology, Evolutionary Biology / Genetics
The extant phylogenetic variability of a given protein contains information about its underlying sequence-fitness landscape, potentially of value to ancestral reconstruction. In extracting such ...
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The extant phylogenetic variability of a given protein contains information about its underlying sequence-fitness landscape, potentially of value to ancestral reconstruction. In extracting such information, it is pertinent to focus on coarse-grained traits of sequence with strong physicochemical bearing on the protein's phenotype. This chapter uses phylogenetic data to stake out roughly the landscape for a protein component of spider silk.Less
The extant phylogenetic variability of a given protein contains information about its underlying sequence-fitness landscape, potentially of value to ancestral reconstruction. In extracting such information, it is pertinent to focus on coarse-grained traits of sequence with strong physicochemical bearing on the protein's phenotype. This chapter uses phylogenetic data to stake out roughly the landscape for a protein component of spider silk.
Lesley J. Collins and Peter J. Lockhart
- Published in print:
- 2007
- Published Online:
- September 2008
- ISBN:
- 9780199299188
- eISBN:
- 9780191714979
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199299188.003.0009
- Subject:
- Biology, Evolutionary Biology / Genetics
A number of authors have recently stressed the importance of understanding the evolution of protein-protein interactions as an underlying cause of covarion-like patterns of evolution in ancestral ...
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A number of authors have recently stressed the importance of understanding the evolution of protein-protein interactions as an underlying cause of covarion-like patterns of evolution in ancestral sequences. Coevolution of interacting partners is seen as important, first in directing the evolution of proteins, and second in explaining why structural constraints may become lineage-specific while function remains the same. Although the concept of heterotachy and covarion evolution in the literature is most often restricted to describing the evolution of orthologs, the same or similar principles of sequence divergence apply to proteins related by gene duplication (paralogs), and which have different functions and functional constraints. This chapter discusses heterotachy and gene finding, gene finding with ancestral sequences, and heterotachy and ancestral state reconstruction.Less
A number of authors have recently stressed the importance of understanding the evolution of protein-protein interactions as an underlying cause of covarion-like patterns of evolution in ancestral sequences. Coevolution of interacting partners is seen as important, first in directing the evolution of proteins, and second in explaining why structural constraints may become lineage-specific while function remains the same. Although the concept of heterotachy and covarion evolution in the literature is most often restricted to describing the evolution of orthologs, the same or similar principles of sequence divergence apply to proteins related by gene duplication (paralogs), and which have different functions and functional constraints. This chapter discusses heterotachy and gene finding, gene finding with ancestral sequences, and heterotachy and ancestral state reconstruction.
Roger W. Shuy
- Published in print:
- 2008
- Published Online:
- May 2008
- ISBN:
- 9780195328837
- eISBN:
- 9780199870165
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195328837.003.0013
- Subject:
- Linguistics, Sociolinguistics / Anthropological Linguistics
A 111-page book about how to increase gas mileage in cars was the alleged source of a one-page promotional piece widely distributed by an oil company. The author and publisher of the book brought a ...
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A 111-page book about how to increase gas mileage in cars was the alleged source of a one-page promotional piece widely distributed by an oil company. The author and publisher of the book brought a copyright infringement suit against the oil company, which in turn countered that the parts it borrowed fell under the copyright fair use doctrine. The author and publisher invoked the legal concepts of proportionality, substantial similarity, and originality. All of the fifty-five “tips” in the defendant's piece were the same as those in the book, effective measures of proportionality and originality. Substantial similarity also was found in the pamphlet's speech acts, speech act sequencing, lexical borrowing, minor changes in grammar such as plural for singular nouns, verb tense, ratios, topics, and topic sequencing.Less
A 111-page book about how to increase gas mileage in cars was the alleged source of a one-page promotional piece widely distributed by an oil company. The author and publisher of the book brought a copyright infringement suit against the oil company, which in turn countered that the parts it borrowed fell under the copyright fair use doctrine. The author and publisher invoked the legal concepts of proportionality, substantial similarity, and originality. All of the fifty-five “tips” in the defendant's piece were the same as those in the book, effective measures of proportionality and originality. Substantial similarity also was found in the pamphlet's speech acts, speech act sequencing, lexical borrowing, minor changes in grammar such as plural for singular nouns, verb tense, ratios, topics, and topic sequencing.
David A. Liberles
- Published in print:
- 2006
- Published Online:
- September 2007
- ISBN:
- 9780199297306
- eISBN:
- 9780191713729
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199297306.003.0010
- Subject:
- Biology, Evolutionary Biology / Genetics
As genome sequencing projects have propagated, comparative genomics has emerged as a method of choice for understanding protein function. There are simple approaches for comparing sequences, like ...
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As genome sequencing projects have propagated, comparative genomics has emerged as a method of choice for understanding protein function. There are simple approaches for comparing sequences, like relative entropy or binary transformations of gene content comparisons. However, phylogenetic methods that explicitly consider evolutionary history are not only more powerful, but enable additional types of analysis drawing on knowledge in parallel fields, such as ecology, anthropology, and geology. This chapter focuses both on methodological issues and on their application to real genomic-scale problems. Parsimony and maximum likelihood are two phylogenetic approaches that are used and often compared side-by-side. While the choice between them has been contentious at times, they frequently give similar results and where they don't, they can complement each other. Maximum likelihood works well when a good model is available. Parsimony works well when a good model does not or can not exist, as for very complex processes, and also along very short branches where multiple events per position (as in a sequence) are extremely infrequent. Both methods can be used to estimate ancestral states in a phylogenetic tree. Parsimony based ancestral character reconstruction is fast and can be performed easily in large scale genomic applications.Less
As genome sequencing projects have propagated, comparative genomics has emerged as a method of choice for understanding protein function. There are simple approaches for comparing sequences, like relative entropy or binary transformations of gene content comparisons. However, phylogenetic methods that explicitly consider evolutionary history are not only more powerful, but enable additional types of analysis drawing on knowledge in parallel fields, such as ecology, anthropology, and geology. This chapter focuses both on methodological issues and on their application to real genomic-scale problems. Parsimony and maximum likelihood are two phylogenetic approaches that are used and often compared side-by-side. While the choice between them has been contentious at times, they frequently give similar results and where they don't, they can complement each other. Maximum likelihood works well when a good model is available. Parsimony works well when a good model does not or can not exist, as for very complex processes, and also along very short branches where multiple events per position (as in a sequence) are extremely infrequent. Both methods can be used to estimate ancestral states in a phylogenetic tree. Parsimony based ancestral character reconstruction is fast and can be performed easily in large scale genomic applications.
Thomas Koshy
- Published in print:
- 2008
- Published Online:
- January 2009
- ISBN:
- 9780195334548
- eISBN:
- 9780199868766
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195334548.001.0001
- Subject:
- Mathematics, Combinatorics / Graph Theory / Discrete Mathematics
Fibonacci and Lucas sequences are “two shining stars in the vast array of integer sequences,” and because of their ubiquitousness, tendency to appear in quite unexpected and unrelated places, ...
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Fibonacci and Lucas sequences are “two shining stars in the vast array of integer sequences,” and because of their ubiquitousness, tendency to appear in quite unexpected and unrelated places, abundant applications, and intriguing properties, they have fascinated amateurs and mathematicians alike. However, Catalan numbers are even more fascinating. Like the North Star in the evening sky, they are a beautiful and bright light in the mathematical heavens. They continue to provide a fertile ground for number theorists, especially, Catalan enthusiasts and computer scientists. Since the publication of Euler's triangulation problem (1751) and Catalan's parenthesization problem (1838), over 400 articles and problems on Catalan numbers have appeared in various periodicals. As Martin Gardner noted, even though many amateurs and mathematicians may know the abc's of Catalan sequence, they may not be familiar with their myriad unexpected occurrences, delightful applications, properties, or the beautiful and surprising relationships among numerous examples. Like Fibonacci and Lucas numbers, Catalan numbers are also an excellent source of fun and excitement. They can be used to generate interesting dividends for students, such as intellectual curiosity, experimentation, pattern recognition, conjecturing, and problem-solving techniques. The central character in the nth Catalan number is the central binomial coefficient. So, Catalan numbers can be extracted from Pascal's triangle. In fact, there are a number of ways they can be read from Pascal's triangle; every one of them is described and exemplified. This brings Catalan numbers a step closer to number-theory enthusiasts, especially.Less
Fibonacci and Lucas sequences are “two shining stars in the vast array of integer sequences,” and because of their ubiquitousness, tendency to appear in quite unexpected and unrelated places, abundant applications, and intriguing properties, they have fascinated amateurs and mathematicians alike. However, Catalan numbers are even more fascinating. Like the North Star in the evening sky, they are a beautiful and bright light in the mathematical heavens. They continue to provide a fertile ground for number theorists, especially, Catalan enthusiasts and computer scientists. Since the publication of Euler's triangulation problem (1751) and Catalan's parenthesization problem (1838), over 400 articles and problems on Catalan numbers have appeared in various periodicals. As Martin Gardner noted, even though many amateurs and mathematicians may know the abc's of Catalan sequence, they may not be familiar with their myriad unexpected occurrences, delightful applications, properties, or the beautiful and surprising relationships among numerous examples. Like Fibonacci and Lucas numbers, Catalan numbers are also an excellent source of fun and excitement. They can be used to generate interesting dividends for students, such as intellectual curiosity, experimentation, pattern recognition, conjecturing, and problem-solving techniques. The central character in the nth Catalan number is the central binomial coefficient. So, Catalan numbers can be extracted from Pascal's triangle. In fact, there are a number of ways they can be read from Pascal's triangle; every one of them is described and exemplified. This brings Catalan numbers a step closer to number-theory enthusiasts, especially.
Alessandro Minelli
- Published in print:
- 2008
- Published Online:
- May 2009
- ISBN:
- 9780198566205
- eISBN:
- 9780191713866
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198566205.003.0002
- Subject:
- Biology, Animal Biology, Evolutionary Biology / Genetics
The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially ...
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The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially increasing amount of molecular sequence data, to be analysed through increasingly sophisticated algorithms. Progress has been overcoming the pitfalls of earlier naïve hypotheses, such as the putatively uniform rate of the molecular clock across lineages, as well as problems deriving from gene duplication, gene loss, and horizontal gene transfer. However, the intrinsic limits of the resolution power of sequence comparisons are also emerging, as in the case of geologically old sequences of a series of branchings of the phylogenetic tree, which reduce in practice to multibranched star-shaped phylogenies. The single best source of data for the molecular phylogeny of the Metazoa is arguably the mitochondrial genome, in terms of gene, genome sequences, and also gene orderLess
The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially increasing amount of molecular sequence data, to be analysed through increasingly sophisticated algorithms. Progress has been overcoming the pitfalls of earlier naïve hypotheses, such as the putatively uniform rate of the molecular clock across lineages, as well as problems deriving from gene duplication, gene loss, and horizontal gene transfer. However, the intrinsic limits of the resolution power of sequence comparisons are also emerging, as in the case of geologically old sequences of a series of branchings of the phylogenetic tree, which reduce in practice to multibranched star-shaped phylogenies. The single best source of data for the molecular phylogeny of the Metazoa is arguably the mitochondrial genome, in terms of gene, genome sequences, and also gene order
