before_sent
stringlengths 0
50.4k
| before_sent_with_intent
stringlengths 10
50.5k
| after_sent
stringlengths 0
50.6k
| labels
stringclasses 5
values | confidence
stringlengths 5
10
| doc_id
stringlengths 2
10
| revision_depth
stringclasses 5
values |
|---|---|---|---|---|---|---|
The numbers of each sort of molecule present in an equilibrium chemical reaction mixture are Poisson distributed . | <clarity> The numbers of each sort of molecule present in an equilibrium chemical reaction mixture are Poisson distributed . | The numbers of each sort of molecule present in an equilibrium chemical reaction mixture , the number of molecules present obeys a Poisson distribution . | clarity | 0.99863297 | 0708.2953 | 1 |
We ask when the same is true of the steady state of a nonequilibrium reaction network and obtain a nearly complete answer. | <meaning-changed> We ask when the same is true of the steady state of a nonequilibrium reaction network and obtain a nearly complete answer. | We ask when the same is true of the steady state of a nonequilibrium reaction network and obtain an essentially complete answer. | meaning-changed | 0.99047196 | 0708.2953 | 1 |
Such driven systems also obey an analog of the fluctuation-dissipation theorem and can equilibrate when in contact with each other . | <clarity> Such driven systems also obey an analog of the fluctuation-dissipation theorem and can equilibrate when in contact with each other . | Such driven systems also obey an analog of the fluctuation-dissipation theorem . | clarity | 0.99896264 | 0708.2953 | 1 |
Our results may be relevant to biological systems and to the larger question of how equilibrium ideas might extend to nonequilibrium systems. | <clarity> Our results may be relevant to biological systems and to the larger question of how equilibrium ideas might extend to nonequilibrium systems. | Our results may be relevant to biological systems and to the larger question of how equilibrium concepts might apply to nonequilibrium systems. | clarity | 0.9987035 | 0708.2953 | 1 |
Using our recent contribution, the " partitioned leaping algorithm" [L. A. Harris and P. Clancy, J. Chem. | <meaning-changed> Using our recent contribution, the " partitioned leaping algorithm" [L. A. Harris and P. Clancy, J. Chem. | " partitioned leaping algorithm" [L. A. Harris and P. Clancy, J. Chem. | meaning-changed | 0.52542514 | 0709.0561 | 1 |
Using our recent contribution, the " partitioned leaping algorithm" [L. A. Harris and P. Clancy, J. Chem. | <meaning-changed> Using our recent contribution, the " partitioned leaping algorithm" [L. A. Harris and P. Clancy, J. Chem. | Using our recent contribution, the " Leaping" methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address this issue using the " partitioned leaping algorithm" [L. A. Harris and P. Clancy, J. Chem. | meaning-changed | 0.99936634 | 0709.0561 | 1 |
Using our recent contribution, the " partitioned leaping algorithm" [L. A. Harris and P. Clancy, J. Chem. | <meaning-changed> Using our recent contribution, the " partitioned leaping algorithm" [L. A. Harris and P. Clancy, J. Chem. | Using our recent contribution, the " partitioned leaping algorithm" (PLA) [L. A. Harris and P. Clancy, J. Chem. | meaning-changed | 0.9993636 | 0709.0561 | 1 |
Phys. 125, 144107 (2006)], we investigate the effects of stochasticity in two model biochemical reaction networks. | <meaning-changed> Phys. 125, 144107 (2006)], we investigate the effects of stochasticity in two model biochemical reaction networks. | Phys. 125, 144107 (2006)], a recently-introduced multiscale leaping approach. We use the PLA to investigate stochastic effects in two model biochemical reaction networks. | meaning-changed | 0.99946636 | 0709.0561 | 1 |
By considering situations both where "leaping" proves beneficial and where it does not, we gain valuable insight that can aid in and advance the use of leaping methods in computational biology. In particular, we identify reaction subnetworks with small populations and large rate constants as a major bottleneck for leaping. We also demonstrate the use of "model reduction" in conjunction with leaping to circumvent this problem and expose a current need in this area: a model-reduction hierarchy analogous to that on which the leaping methods are based D. T. Gillespie, J. Chem. | <meaning-changed> By considering situations both where "leaping" proves beneficial and where it does not, we gain valuable insight that can aid in and advance the use of leaping methods in computational biology. In particular, we identify reaction subnetworks with small populations and large rate constants as a major bottleneck for leaping. We also demonstrate the use of "model reduction" in conjunction with leaping to circumvent this problem and expose a current need in this area: a model-reduction hierarchy analogous to that on which the leaping methods are based D. T. Gillespie, J. Chem. | D. T. Gillespie, J. Chem. | meaning-changed | 0.7374294 | 0709.0561 | 1 |
We also demonstrate the use of "model reduction" in conjunction with leaping to circumvent this problem and expose a current need in this area: a model-reduction hierarchy analogous to that on which the leaping methods are based D. T. Gillespie, J. Chem. Phys. 113, 297 (2000); 115, 1716 (2001)%DIFDELCMD < ]%%% . In situations where leaping is seen to perform well, we emphasize the significant advantages to using these methods over more traditional simulation approaches. | <coherence> We also demonstrate the use of "model reduction" in conjunction with leaping to circumvent this problem and expose a current need in this area: a model-reduction hierarchy analogous to that on which the leaping methods are based D. T. Gillespie, J. Chem. Phys. 113, 297 (2000); 115, 1716 (2001)%DIFDELCMD < ]%%% . In situations where leaping is seen to perform well, we emphasize the significant advantages to using these methods over more traditional simulation approaches. | We also demonstrate the use of "model reduction" in conjunction with leaping to circumvent this problem and expose a current need in this area: a model-reduction hierarchy analogous to that on which the leaping methods are based %DIFDELCMD < ]%%% . In situations where leaping is seen to perform well, we emphasize the significant advantages to using these methods over more traditional simulation approaches. | coherence | 0.99410003 | 0709.0561 | 1 |
115, 1716 (2001)%DIFDELCMD < ]%%% . In situations where leaping is seen to perform well, we emphasize the significant advantages to using these methods over more traditional simulation approaches. We show how leaping allows for statistical investigations beyond the reach of "exact-stochastic" methods and demonstrate how one can uncover, via such investigations, subtle stochastic effects that would be ignored in deterministic treatments. | <clarity> 115, 1716 (2001)%DIFDELCMD < ]%%% . In situations where leaping is seen to perform well, we emphasize the significant advantages to using these methods over more traditional simulation approaches. We show how leaping allows for statistical investigations beyond the reach of "exact-stochastic" methods and demonstrate how one can uncover, via such investigations, subtle stochastic effects that would be ignored in deterministic treatments. | 115, 1716 (2001)%DIFDELCMD < ]%%% The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to test the limits of the leaping approach. We demonstrate how the PLA allows us to quantify subtle effects of stochasticity that would be ignored in deterministic treatments. | clarity | 0.9968154 | 0709.0561 | 1 |
We show how leaping allows for statistical investigations beyond the reach of "exact-stochastic" methods and demonstrate how one can uncover, via such investigations, subtle stochastic effects that would be ignored in deterministic treatments. We then show, using examples taken from the literature, that conditions identified here as lending well to leaping do, in fact, arise in natural biological systems. This leads us to discuss and demonstrate how the statistical information garnered from a leaping study can be used to infer mechanistic details of a biological process and motivate experiments . | <clarity> We show how leaping allows for statistical investigations beyond the reach of "exact-stochastic" methods and demonstrate how one can uncover, via such investigations, subtle stochastic effects that would be ignored in deterministic treatments. We then show, using examples taken from the literature, that conditions identified here as lending well to leaping do, in fact, arise in natural biological systems. This leads us to discuss and demonstrate how the statistical information garnered from a leaping study can be used to infer mechanistic details of a biological process and motivate experiments . | We show how leaping allows for statistical investigations beyond the reach of "exact-stochastic" methods and demonstrate how one can uncover, via such investigations, subtle stochastic effects that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly-used "exact" stochastic methods. We also illustrate prime bottlenecks that can hinder the approach and discuss possible strategies for overcoming them . | clarity | 0.99809784 | 0709.0561 | 1 |
Overall, we demonstrate to biologists the great potential that leaping methods hold for real-world biological research while highlighting to algorithmists areas still in need of improvement . | <clarity> Overall, we demonstrate to biologists the great potential that leaping methods hold for real-world biological research while highlighting to algorithmists areas still in need of improvement . | Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while also elucidating the obstacles that one can expect to encounter . | clarity | 0.9968359 | 0709.0561 | 1 |
The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to test the limits of the leaping approach . | <meaning-changed> The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to test the limits of the leaping approach . | The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to be generally representative of real biological systems . | meaning-changed | 0.9977975 | 0709.0561 | 2 |
We demonstrate how the PLA allows us to quantify subtle effects of stochasticity that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly-used "exact" stochastic methods. | <meaning-changed> We demonstrate how the PLA allows us to quantify subtle effects of stochasticity that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly-used "exact" stochastic methods. | We demonstrate how the PLA allows us to quantify subtle effects of stochasticity in these systems that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly-used "exact" stochastic methods. | meaning-changed | 0.9779183 | 0709.0561 | 2 |
We also illustrate prime bottlenecks that can hinder the approach and discuss possible strategies for overcoming them. | <clarity> We also illustrate prime bottlenecks that can hinder the approach and discuss possible strategies for overcoming them. | We also illustrate bottlenecks that can hinder the approach and discuss possible strategies for overcoming them. | clarity | 0.9961247 | 0709.0561 | 2 |
We also illustrate prime bottlenecks that can hinder the approach and discuss possible strategies for overcoming them. | <clarity> We also illustrate prime bottlenecks that can hinder the approach and discuss possible strategies for overcoming them. | We also illustrate prime bottlenecks that can hinder the approach and exemplify and discuss possible strategies for overcoming them. | clarity | 0.92131287 | 0709.0561 | 2 |
Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while also elucidating the obstacles that one can expect to encounter . | <clarity> Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while also elucidating the obstacles that one can expect to encounter . | Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while at the same time elucidating obstacles that are often encountered in practice . | clarity | 0.9980248 | 0709.0561 | 2 |
The major objective of this paper is to introduce a novel method for the functional annotation of genes. Our method is based on a graph theoretical measure we call joint betweenness, which is an extension of the well known betweenness centrality measure, involving pairs of genes. We apply our method to the transcriptional regulatory network of yeast to, first, provide a large scale proof of concept of our method and, second, make predictions about the biological function of previously unknown genes . | <coherence> The major objective of this paper is to introduce a novel method for the functional annotation of genes. Our method is based on a graph theoretical measure we call joint betweenness, which is an extension of the well known betweenness centrality measure, involving pairs of genes. We apply our method to the transcriptional regulatory network of yeast to, first, provide a large scale proof of concept of our method and, second, make predictions about the biological function of previously unknown genes . | This paper has been withdrawn . | coherence | 0.99628603 | 0709.3291 | 1 |
We find that discrete noise of inhibiting (signal) molecules can greatly delay the extinction of a regulated component in a prototypical biochemical regulatory network. | <clarity> We find that discrete noise of inhibiting (signal) molecules can greatly delay the extinction of a regulated component in a prototypical biochemical regulatory network. | We find that discrete noise of inhibiting (signal) molecules can greatly delay the extinction of plasmids in a plasmid replication system: a prototypical biochemical regulatory network. | clarity | 0.99822694 | 0709.3606 | 1 |
We calculate analytically the probability distribution of the metastable state of the regulated component and show that deterministic reaction rate equations may fail in predicting the average number of regulated molecules even when this number is large, and the time is short compared to the mean extinction time. | <clarity> We calculate analytically the probability distribution of the metastable state of the regulated component and show that deterministic reaction rate equations may fail in predicting the average number of regulated molecules even when this number is large, and the time is short compared to the mean extinction time. | We calculate the probability distribution of the metastable state of the regulated component and show that deterministic reaction rate equations may fail in predicting the average number of regulated molecules even when this number is large, and the time is short compared to the mean extinction time. | clarity | 0.9934216 | 0709.3606 | 1 |
We calculate analytically the probability distribution of the metastable state of the regulated component and show that deterministic reaction rate equations may fail in predicting the average number of regulated molecules even when this number is large, and the time is short compared to the mean extinction time. | <meaning-changed> We calculate analytically the probability distribution of the metastable state of the regulated component and show that deterministic reaction rate equations may fail in predicting the average number of regulated molecules even when this number is large, and the time is short compared to the mean extinction time. | We calculate analytically the probability distribution of the metastable state of the plasmids and show on this example that the reaction rate equations may fail in predicting the average number of regulated molecules even when this number is large, and the time is short compared to the mean extinction time. | meaning-changed | 0.9590948 | 0709.3606 | 1 |
We calculate analytically the probability distribution of the metastable state of the regulated component and show that deterministic reaction rate equations may fail in predicting the average number of regulated molecules even when this number is large, and the time is short compared to the mean extinction time. | <clarity> We calculate analytically the probability distribution of the metastable state of the regulated component and show that deterministic reaction rate equations may fail in predicting the average number of regulated molecules even when this number is large, and the time is short compared to the mean extinction time. | We calculate analytically the probability distribution of the metastable state of the regulated component and show that deterministic reaction rate equations may fail in predicting the average number of regulated molecules even when this number is large, and the time is much shorter than the mean extinction time. | clarity | 0.9977792 | 0709.3606 | 1 |
Microtubules (MTs), nano-tubes which act as struts in the scaffolding of eucaryotic cells, also serve as tracks for intracellular molecular motor transport in eucaryotic cells. In many biological processes, the length distribution of the MTs is controlled by a class of motor proteins called depolymerases (DPs). | <clarity> Microtubules (MTs), nano-tubes which act as struts in the scaffolding of eucaryotic cells, also serve as tracks for intracellular molecular motor transport in eucaryotic cells. In many biological processes, the length distribution of the MTs is controlled by a class of motor proteins called depolymerases (DPs). | In many intracellular processes, the length distribution of the MTs is controlled by a class of motor proteins called depolymerases (DPs). | clarity | 0.99879336 | 0709.3675 | 1 |
In many biological processes, the length distribution of the MTs is controlled by a class of motor proteins called depolymerases (DPs). | <clarity> In many biological processes, the length distribution of the MTs is controlled by a class of motor proteins called depolymerases (DPs). | In many biological processes, the length distribution of microtubules is controlled by a class of motor proteins called depolymerases (DPs). | clarity | 0.9900731 | 0709.3675 | 1 |
In many biological processes, the length distribution of the MTs is controlled by a class of motor proteins called depolymerases (DPs). A DP diffuses or walks along a MT to reach one of the tips of the MT andthen begins depolymerizing the MT itself . | <meaning-changed> In many biological processes, the length distribution of the MTs is controlled by a class of motor proteins called depolymerases (DPs). A DP diffuses or walks along a MT to reach one of the tips of the MT andthen begins depolymerizing the MT itself . | In many biological processes, the length distribution of the MTs is controlled by a class of motor proteins , called depolymerases. Experiments have shown that, following binding to the MT andthen begins depolymerizing the MT itself . | meaning-changed | 0.99491596 | 0709.3675 | 1 |
A DP diffuses or walks along a MT to reach one of the tips of the MT andthen begins depolymerizing the MT itself . | <clarity> A DP diffuses or walks along a MT to reach one of the tips of the MT andthen begins depolymerizing the MT itself . | A DP diffuses or walks along a MT to reach one of the tips of the surface of a microtubule, depolymerases are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there . | clarity | 0.6876278 | 0709.3675 | 1 |
We develop a quantitative model that captures both these processes within a single theoretical framework. We show that the action of both diffusing and walking DPs leads to a length-dependent depolymerization of the MT; however, their effects on the length distribution are different. | <clarity> We develop a quantitative model that captures both these processes within a single theoretical framework. We show that the action of both diffusing and walking DPs leads to a length-dependent depolymerization of the MT; however, their effects on the length distribution are different. | We develop a quantitative model to study the depolymerizing action of such a generic motor protein, and its possible effects on the length distribution are different. | clarity | 0.9982723 | 0709.3675 | 1 |
however, their effects on the length distribution are different. Under experimental conditions, the diffusing DP produces a non-monotonic distribution of lengths as opposed to a nearly exponential distribution in the case of the walking DP. | <meaning-changed> however, their effects on the length distribution are different. Under experimental conditions, the diffusing DP produces a non-monotonic distribution of lengths as opposed to a nearly exponential distribution in the case of the walking DP. | however, their effects on the length distribution of microtubules. We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the distribution is non-monotonic distribution of lengths as opposed to a nearly exponential distribution in the case of the walking DP. | meaning-changed | 0.9992342 | 0709.3675 | 1 |
Under experimental conditions, the diffusing DP produces a non-monotonic distribution of lengths as opposed to a nearly exponential distribution in the case of the walking DP. The former also shows a minimum in the r.m.s fluctuation to mean ratio of the length against the DP concentration, while the latter does not. Our findings imply that a diffusing DP, like MCAK, might be used by the cell for precise length control during cell division, while a walking DP, like Kip3p, would be more useful for fast depolymerization . | <clarity> Under experimental conditions, the diffusing DP produces a non-monotonic distribution of lengths as opposed to a nearly exponential distribution in the case of the walking DP. The former also shows a minimum in the r.m.s fluctuation to mean ratio of the length against the DP concentration, while the latter does not. Our findings imply that a diffusing DP, like MCAK, might be used by the cell for precise length control during cell division, while a walking DP, like Kip3p, would be more useful for fast depolymerization . | Under experimental conditions, the diffusing DP produces a non-monotonic provided the motor processivity is sufficiently small. Our findings suggest that such motor proteins have a central role in ensuring precise control of MT lengths . | clarity | 0.98693347 | 0709.3675 | 1 |
In many intracellular processes, the length distribution of microtubules is controlled by a class of motor proteins, called depolymerases . Experiments have shown that, following binding to the surface of a microtubule, depolymerases are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. | <clarity> In many intracellular processes, the length distribution of microtubules is controlled by a class of motor proteins, called depolymerases . Experiments have shown that, following binding to the surface of a microtubule, depolymerases are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. | In many intracellular processes, the length distribution of microtubules is controlled by depolymerizing motor proteins . Experiments have shown that, following binding to the surface of a microtubule, depolymerases are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. | clarity | 0.9985129 | 0709.3675 | 2 |
In many intracellular processes, the length distribution of microtubules is controlled by a class of motor proteins, called depolymerases . Experiments have shown that, following binding to the surface of a microtubule, depolymerases are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. | <meaning-changed> In many intracellular processes, the length distribution of microtubules is controlled by a class of motor proteins, called depolymerases . Experiments have shown that, following binding to the surface of a microtubule, depolymerases are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. | In many intracellular processes, the length distribution of microtubules is controlled by a class of motor proteins, called depolymerases . Experiments have shown that, following non-specific binding to the surface of a microtubule, depolymerases are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. | meaning-changed | 0.99627787 | 0709.3675 | 2 |
In many intracellular processes, the length distribution of microtubules is controlled by a class of motor proteins, called depolymerases . Experiments have shown that, following binding to the surface of a microtubule, depolymerases are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. | <clarity> In many intracellular processes, the length distribution of microtubules is controlled by a class of motor proteins, called depolymerases . Experiments have shown that, following binding to the surface of a microtubule, depolymerases are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. | In many intracellular processes, the length distribution of microtubules is controlled by a class of motor proteins, called depolymerases . Experiments have shown that, following binding to the surface of a microtubule, depolymerizers are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. | clarity | 0.9752348 | 0709.3675 | 2 |
We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the distribution is non-monotonic provided the motor processivity is sufficiently small . | <clarity> We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the distribution is non-monotonic provided the motor processivity is sufficiently small . | We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the length distribution is, in general, non-monotonic provided the motor processivity is sufficiently small . | clarity | 0.9507628 | 0709.3675 | 2 |
We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the distribution is non-monotonic provided the motor processivity is sufficiently small . | <meaning-changed> We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the distribution is non-monotonic provided the motor processivity is sufficiently small . | We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the distribution is non-monotonic with a single peak. However, for highly processive motors and large motor densities, this distribution effectively becomes an exponential decay . | meaning-changed | 0.9993088 | 0709.3675 | 2 |
Our findings suggest that such motor proteins have a central role in ensuring precise control of MT lengths . | <clarity> Our findings suggest that such motor proteins have a central role in ensuring precise control of MT lengths . | Our findings suggest that such motor proteins may be selectively used by the cell to ensure precise control of MT lengths . | clarity | 0.99169534 | 0709.3675 | 2 |
Our findings suggest that such motor proteins have a central role in ensuring precise control of MT lengths . | <meaning-changed> Our findings suggest that such motor proteins have a central role in ensuring precise control of MT lengths . | Our findings suggest that such motor proteins have a central role in ensuring precise control of MT lengths . The model is also used to analyze experimental observations of motor-induced depolymerization . | meaning-changed | 0.99950683 | 0709.3675 | 2 |
We develop a network-based algorithm to predict and verify indirect regulatory interactions in a large-scale genetic regulatory network. | <clarity> We develop a network-based algorithm to predict and verify indirect regulatory interactions in a large-scale genetic regulatory network. | We develop a matrix-based approach to predict and verify indirect regulatory interactions in a large-scale genetic regulatory network. | clarity | 0.99154294 | 0710.0892 | 1 |
We develop a network-based algorithm to predict and verify indirect regulatory interactions in a large-scale genetic regulatory network. Indirect regulations are important as they constitute the majority of experimental data. Our approach is based on the network topology and can be easily incorporated using a matrix formalism. | <clarity> We develop a network-based algorithm to predict and verify indirect regulatory interactions in a large-scale genetic regulatory network. Indirect regulations are important as they constitute the majority of experimental data. Our approach is based on the network topology and can be easily incorporated using a matrix formalism. | We develop a network-based algorithm to predict and verify indirect interactions in gene and protein regulatory networks. It is based on the network topology and can be easily incorporated using a matrix formalism. | clarity | 0.99882716 | 0710.0892 | 1 |
Our approach is based on the network topology and can be easily incorporated using a matrix formalism. The essence of the method is to extend the transitivity of indirect regulations ( i.e. | <clarity> Our approach is based on the network topology and can be easily incorporated using a matrix formalism. The essence of the method is to extend the transitivity of indirect regulations ( i.e. | Our approach is based on the approximate transitivity of indirect regulations ( i.e. | clarity | 0.9977289 | 0710.0892 | 1 |
The essence of the method is to extend the transitivity of indirect regulations ( i.e. | <coherence> The essence of the method is to extend the transitivity of indirect regulations ( i.e. | The essence of the method is to extend the transitivity of indirect regulations ( e.g. | coherence | 0.4930237 | 0710.0892 | 1 |
A regulates B and B regulates C implies A regulates C) to longer cascades and effectively take care of the signs of the regulations. | <clarity> A regulates B and B regulates C implies A regulates C) to longer cascades and effectively take care of the signs of the regulations. | A regulates B and B regulates C often implies that A regulates C) to longer cascades and effectively take care of the signs of the regulations. | clarity | 0.9848011 | 0710.0892 | 1 |
A regulates B and B regulates C implies A regulates C) to longer cascades and effectively take care of the signs of the regulations. This algorithm is tailored for large and heavily interconnected networks, which are of growing importance due to the accruement of data from high-throughput experiments. We apply the algorithm to the regulatory networks of Homo sapiens, Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster , resulting in novel predictions with calibrated reliability . | <meaning-changed> A regulates B and B regulates C implies A regulates C) to longer cascades and effectively take care of the signs of the regulations. This algorithm is tailored for large and heavily interconnected networks, which are of growing importance due to the accruement of data from high-throughput experiments. We apply the algorithm to the regulatory networks of Homo sapiens, Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster , resulting in novel predictions with calibrated reliability . | A regulates B and B regulates C implies A regulates C) and optimally takes into account the length of a cascade and signs of intermediate interactions. Our method is at its most powerful when applied to large and densely interconnected networks. It successfully predicts both the yet unknown indirect regulations, as well as the sign (activation or repression) of already known ones. The reliability of sign predictions was calibrated using the gold-standard sets of positive and negative interactions. We fine-tuned the parameters of our algorithm by maximizing the area under the Receiver Operating Characteristic (ROC) curve. We then applied the optimized algorithm to large literature-derived networks of all direct and indirect regulatory interactions in several URLanisms ( Homo sapiens, Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster , resulting in novel predictions with calibrated reliability . | meaning-changed | 0.99915874 | 0710.0892 | 1 |
We apply the algorithm to the regulatory networks of Homo sapiens, Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster , resulting in novel predictions with calibrated reliability . | <coherence> We apply the algorithm to the regulatory networks of Homo sapiens, Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster , resulting in novel predictions with calibrated reliability . | We apply the algorithm to the regulatory networks of Homo sapiens, Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster ) . | coherence | 0.94328904 | 0710.0892 | 1 |
However the use of a standard t copula is often criticized due to its restriction of having a single parameter for the degrees of freedom (dof) that may limit its capability to model the tail dependence structure in a multivariate case. | <fluency> However the use of a standard t copula is often criticized due to its restriction of having a single parameter for the degrees of freedom (dof) that may limit its capability to model the tail dependence structure in a multivariate case. | However , the use of a standard t copula is often criticized due to its restriction of having a single parameter for the degrees of freedom (dof) that may limit its capability to model the tail dependence structure in a multivariate case. | fluency | 0.99850106 | 0710.3959 | 1 |
To overcome this problem, grouped t copula was proposed recently where risks are grouped a priori in such a way that each group has a standard t copula with its specific dof parameter. | <fluency> To overcome this problem, grouped t copula was proposed recently where risks are grouped a priori in such a way that each group has a standard t copula with its specific dof parameter. | To overcome this problem, grouped t copula was proposed recently , where risks are grouped a priori in such a way that each group has a standard t copula with its specific dof parameter. | fluency | 0.99936134 | 0710.3959 | 1 |
In this paper we propose the use of a new t copula, generalizing grouped t copula to have each group consisting of one risk only, so that a priori grouping is not required. | <coherence> In this paper we propose the use of a new t copula, generalizing grouped t copula to have each group consisting of one risk only, so that a priori grouping is not required. | In this paper we propose the use of a grouped t copula to have each group consisting of one risk only, so that a priori grouping is not required. | coherence | 0.9589543 | 0710.3959 | 1 |
In this paper we propose the use of a new t copula, generalizing grouped t copula to have each group consisting of one risk only, so that a priori grouping is not required. | <clarity> In this paper we propose the use of a new t copula, generalizing grouped t copula to have each group consisting of one risk only, so that a priori grouping is not required. | In this paper we propose the use of a new t copula, generalizing grouped t copula , where each group consists of one risk only, so that a priori grouping is not required. | clarity | 0.8994213 | 0710.3959 | 1 |
In this paper we propose the use of a new t copula, generalizing grouped t copula to have each group consisting of one risk only, so that a priori grouping is not required. | <clarity> In this paper we propose the use of a new t copula, generalizing grouped t copula to have each group consisting of one risk only, so that a priori grouping is not required. | In this paper we propose the use of a new t copula, generalizing grouped t copula to have each group consisting of one risk factor only, so that a priori grouping is not required. | clarity | 0.9766258 | 0710.3959 | 1 |
The characteristics of this copula in the bivariate case are described . | <clarity> The characteristics of this copula in the bivariate case are described . | The copula characteristics in the bivariate case are described . | clarity | 0.99872845 | 0710.3959 | 1 |
The characteristics of this copula in the bivariate case are described . | <clarity> The characteristics of this copula in the bivariate case are described . | The characteristics of this copula in the bivariate case are studied . | clarity | 0.99847335 | 0710.3959 | 1 |
We explain simulation and calibration procedures and provide examples . | <meaning-changed> We explain simulation and calibration procedures and provide examples . | We explain simulation and calibration procedures , including a simulation study on finite sample properties of the maximum likelihood estimators and Kendall's tau approximation. This new copula can be significantly different from the standard t copula in terms of risk measures such as tail dependence, value at risk and expected shortfall. Keywords: grouped t copula, tail dependence, risk management . | meaning-changed | 0.99943644 | 0710.3959 | 1 |
Stimulated by the long term goal of identifying gene targets for corn crop improvement, we perturbed a simple plant cell system by the addition of abscisic acid, a well-characterized plant hormone, and measured the gene expression with transcriptional microarrays for 150 minutes, every 10 minutes after treatment. Parameters of biochemistry-based models were inferred for 25 downstream (regulated) genes of interest using a thoroughly studied approximation of the posterior distribution, accounting for model uncertainty through Bayesian model averaging. The four causal gene interactions thereby identified as probable under a first-order difference model present testable hypotheses for future experimentation that could conceivably build knowledge of the complex biological system. The small scale of this result compared to many of the reconstructed networks reported in recent literature reflects a cautious approach to systems biology, but without a priori skepticism. The number of putative genes represented on the microarrays used is on the order of the size of the genome; a modification of the methodology for cases in which the number of measured genes is a small fraction of the genome size is also provided. For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | <coherence> Stimulated by the long term goal of identifying gene targets for corn crop improvement, we perturbed a simple plant cell system by the addition of abscisic acid, a well-characterized plant hormone, and measured the gene expression with transcriptional microarrays for 150 minutes, every 10 minutes after treatment. Parameters of biochemistry-based models were inferred for 25 downstream (regulated) genes of interest using a thoroughly studied approximation of the posterior distribution, accounting for model uncertainty through Bayesian model averaging. The four causal gene interactions thereby identified as probable under a first-order difference model present testable hypotheses for future experimentation that could conceivably build knowledge of the complex biological system. The small scale of this result compared to many of the reconstructed networks reported in recent literature reflects a cautious approach to systems biology, but without a priori skepticism. The number of putative genes represented on the microarrays used is on the order of the size of the genome; a modification of the methodology for cases in which the number of measured genes is a small fraction of the genome size is also provided. For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential equations that describe transcriptional kinetics. Practical approximations of kinetic models would enable inferring causal relationships between genes from expression data of microarray, tag-based and conventional platforms, but conclusions are sensitive to the assumptions made. Results: The representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | coherence | 0.9562627 | 0710.4127 | 1 |
For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | <clarity> For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a sufficiently large portion of genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | clarity | 0.99809843 | 0710.4127 | 1 |
For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | <clarity> For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an upper bound on how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | clarity | 0.99852043 | 0710.4127 | 1 |
For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | <clarity> For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may place in influences between genes on the basis of observed data. | clarity | 0.99830854 | 0710.4127 | 1 |
For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | <meaning-changed> For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of observed data. | For purposes of inferring biological networks, the main advantage of microarray technology over low-throughput methods may be that the representation of a large enough portion of the genome enables computation of an informative upper bound of how much confidence one may reasonably place in causal relationships between genes on the basis of expression data. Information about which genes encode transcription factors is not necessary but may be incorporated if available. The methodology is generalized to cover cases in which expression measurements are missing for many of the genes that might control the transcription of the genes of interest. The assumption that the gene expression level is roughly proportional to the rate of translation led to better empirical performance than did either the assumption that the gene expression level is roughly proportional to the protein level or the Bayesian model average of both assumptions. Availability: URL points to R code implementing the methods (R Development Core Team 2004). Supplementary information: URL | meaning-changed | 0.99937636 | 0710.4127 | 1 |
We present a theoretical investigation of the folding of small proteins assisted by chaperones. | <clarity> We present a theoretical investigation of the folding of small proteins assisted by chaperones. | We present a theoretical study of the folding of small proteins assisted by chaperones. | clarity | 0.9983339 | 0711.0916 | 1 |
We present a theoretical investigation of the folding of small proteins assisted by chaperones. We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it . | <clarity> We present a theoretical investigation of the folding of small proteins assisted by chaperones. We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it . | We present a theoretical investigation of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it . | clarity | 0.94998664 | 0711.0916 | 1 |
We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it . | <meaning-changed> We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it . | We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not need any{\it . | meaning-changed | 0.9992798 | 0711.0916 | 1 |
We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it . | <meaning-changed> We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it . | We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it a priori . | meaning-changed | 0.9993561 | 0711.0916 | 1 |
We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it . | <meaning-changed> We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it . | We describe the proteins in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom {\it information about the native state. Hydrogen bonds, dipole-dipole- and hydrophobic interactions are taken explicitly into account. An interesting feature displayed by this potential is the presence of some intermediates between the unfolded and native states. We consider different types of confining potentials in order to study the structural properties of proteins folding inside cages with repulsive or attractive walls . | meaning-changed | 0.9994661 | 0711.0916 | 1 |
The cage of chaperonins is modeled by an external confining potential which is also able to take into account hydrophobic and hydrophilic effects inside the cavity. | <coherence> The cage of chaperonins is modeled by an external confining potential which is also able to take into account hydrophobic and hydrophilic effects inside the cavity. | coherence | 0.70666206 | 0711.0916 | 1 |
|
Using the Wang-Landau algorithm Phys. Rev. Lett. | <coherence> Using the Wang-Landau algorithm Phys. Rev. Lett. | Using the Wang-Landau algorithm | coherence | 0.5964542 | 0711.0916 | 1 |
%DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | <meaning-changed> %DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | %DIFDELCMD < {\bf %%% , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | meaning-changed | 0.953227 | 0711.0916 | 1 |
%DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | <coherence> %DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | %DIFDELCMD < {\bf %%% 86 we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | coherence | 0.992855 | 0711.0916 | 1 |
%DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | <meaning-changed> %DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | %DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states (DOS ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | meaning-changed | 0.9955273 | 0711.0916 | 1 |
%DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | <fluency> %DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cage . | %DIFDELCMD < {\bf %%% 86 , 2050 (2001) we determine the density of states g(E ) and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cages . | fluency | 0.99830556 | 0711.0916 | 1 |
We show how the confinement through the chaperon dramatically reduces the phase space available for the protein leading to a much faster folding process. | <clarity> We show how the confinement through the chaperon dramatically reduces the phase space available for the protein leading to a much faster folding process. | We show that confinement dramatically reduces the phase space available for the protein leading to a much faster folding process. | clarity | 0.9950867 | 0711.0916 | 1 |
We show how the confinement through the chaperon dramatically reduces the phase space available for the protein leading to a much faster folding process. Slightly hydrophobic cages seem to make the native structure more stable . | <meaning-changed> We show how the confinement through the chaperon dramatically reduces the phase space available for the protein leading to a much faster folding process. Slightly hydrophobic cages seem to make the native structure more stable . | We show how the confinement through the chaperon dramatically reduces the phase space available to the protein and that the presence of intermediate states can be controlled by varying the properties of the confining potential. Cages with strongly attractive walls lead to the disappearance of the intermediate states and to a two-state folding into a less stable configuration. However, cages with slightly attractive walls make the native structure more stable . | meaning-changed | 0.99937505 | 0711.0916 | 1 |
Slightly hydrophobic cages seem to make the native structure more stable . However, not any confining potential helps folding . If the inner walls of the cage are strongly hydrophobic, a denaturation process is induced, in which the proteins partially unfold and stick to the walls . | <meaning-changed> Slightly hydrophobic cages seem to make the native structure more stable . However, not any confining potential helps folding . If the inner walls of the cage are strongly hydrophobic, a denaturation process is induced, in which the proteins partially unfold and stick to the walls . | Slightly hydrophobic cages seem to make the native structure more stable than in the case of pure repulsive potentials, and the folding process occurs through intermediate configurations. In order to test the metastable states we analyze the free energy landscapes as a function of the configurational energy and of the end-to-end distance as an order parameter . | meaning-changed | 0.99939907 | 0711.0916 | 1 |
We solve these equations for different contract specifications in a particular but exemplifying case. | <clarity> We solve these equations for different contract specifications in a particular but exemplifying case. | We solve these equations for typical contract specifications, in a particular but exemplifying case. | clarity | 0.84604186 | 0711.2624 | 1 |
We recover the celebrated results for the Wiener process under certain limits. | <meaning-changed> We recover the celebrated results for the Wiener process under certain limits. | We also show how a formal general solution can be found for more exotic derivatives, and we compare prices for alternative models of the underlying. Finally, we recover the celebrated results for the Wiener process under certain limits. | meaning-changed | 0.99944204 | 0711.2624 | 1 |
In this paper we will develop an original approach, based in the use of renewal equations, for obtaining pricing expressions for financial instruments whose underlying asset can be solely described through a simple continuous-time random walk (CTRW) . This enhances the potential use of CTRW techniques in finance. | <clarity> In this paper we will develop an original approach, based in the use of renewal equations, for obtaining pricing expressions for financial instruments whose underlying asset can be solely described through a simple continuous-time random walk (CTRW) . This enhances the potential use of CTRW techniques in finance. | In this paper we will develop a methodology for obtaining pricing expressions for financial instruments whose underlying asset can be solely described through a simple continuous-time random walk (CTRW) . This enhances the potential use of CTRW techniques in finance. | clarity | 0.99852186 | 0711.2624 | 2 |
In this paper we will develop an original approach, based in the use of renewal equations, for obtaining pricing expressions for financial instruments whose underlying asset can be solely described through a simple continuous-time random walk (CTRW) . This enhances the potential use of CTRW techniques in finance. | <clarity> In this paper we will develop an original approach, based in the use of renewal equations, for obtaining pricing expressions for financial instruments whose underlying asset can be solely described through a simple continuous-time random walk (CTRW) . This enhances the potential use of CTRW techniques in finance. | In this paper we will develop an original approach, based in the use of renewal equations, for obtaining pricing expressions for financial instruments whose underlying asset can be described through a simple continuous-time random walk (CTRW) . This enhances the potential use of CTRW techniques in finance. | clarity | 0.9983961 | 0711.2624 | 2 |
In this paper we will develop an original approach, based in the use of renewal equations, for obtaining pricing expressions for financial instruments whose underlying asset can be solely described through a simple continuous-time random walk (CTRW) . This enhances the potential use of CTRW techniques in finance. | <meaning-changed> In this paper we will develop an original approach, based in the use of renewal equations, for obtaining pricing expressions for financial instruments whose underlying asset can be solely described through a simple continuous-time random walk (CTRW) . This enhances the potential use of CTRW techniques in finance. | In this paper we will develop an original approach, based in the use of renewal equations, for obtaining pricing expressions for financial instruments whose underlying asset can be solely described through a simple continuous-time random walk (CTRW) market model. Our approach is very natural to the issue because it is based in the use of renewal equations, and therefore it enhances the potential use of CTRW techniques in finance. | meaning-changed | 0.9993363 | 0711.2624 | 2 |
In this paper, we consider systems with positive feedback interconnections among all variables , which in a continuous setting guarantees a very stable dynamics. | <meaning-changed> In this paper, we consider systems with positive feedback interconnections among all variables , which in a continuous setting guarantees a very stable dynamics. | In this paper, we consider systems with positive feedback interconnections among all variables (known as cooperative systems) , which in a continuous setting guarantees a very stable dynamics. | meaning-changed | 0.9994357 | 0711.2799 | 1 |
We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | <clarity> We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | We show that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | clarity | 0.99722666 | 0711.2799 | 1 |
We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | <meaning-changed> We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional cooperative Boolean networks in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | meaning-changed | 0.69262564 | 0711.2799 | 1 |
We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | <fluency> We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | fluency | 0.93299776 | 0711.2799 | 1 |
We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | <fluency> We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two and which nevertheless contain periodic orbits of length at least c^n. | We present a construction that shows that for an arbitrary constant 0<c<2 and sufficiently large n there exist n-dimensional Boolean networks with this property in which both the indegree and outdegree of each for each variable is bounded by two , and which nevertheless contain periodic orbits of length at least c^n. | fluency | 0.9992812 | 0711.2799 | 1 |
Experiments in recent years have vividly demonstrated that gene expression can Hobe highly stochastic. | <fluency> Experiments in recent years have vividly demonstrated that gene expression can Hobe highly stochastic. | Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. | fluency | 0.999253 | 0711.3812 | 1 |
Only when the correlation time of the fluctuations is long compared to the cell cycle time, do they affect the population's growth rate. | <coherence> Only when the correlation time of the fluctuations is long compared to the cell cycle time, do they affect the population's growth rate. | coherence | 0.99854785 | 0711.3812 | 1 |
|
We also apply our model to perform a cost-benefit analysis of gene regulatory control. | <meaning-changed> We also apply our model to perform a cost-benefit analysis of gene regulatory control. | The model also shows that the ensemble or population average of a quantity, such as the average protein expression level or its variance, is in general not equal to its time average as obtained from tracing a single cell and its descendants. We apply our model to perform a cost-benefit analysis of gene regulatory control. | meaning-changed | 0.9668452 | 0711.3812 | 1 |
With asset prices undergoing a multiplicative random process , we derive approximate analytical results for the optimal investment fractions under various constraints . | <clarity> With asset prices undergoing a multiplicative random process , we derive approximate analytical results for the optimal investment fractions under various constraints . | For lognormally distributed asset returns , we derive approximate analytical results for the optimal investment fractions under various constraints . | clarity | 0.98006403 | 0712.2771 | 1 |
With asset prices undergoing a multiplicative random process , we derive approximate analytical results for the optimal investment fractions under various constraints . | <clarity> With asset prices undergoing a multiplicative random process , we derive approximate analytical results for the optimal investment fractions under various constraints . | With asset prices undergoing a multiplicative random process , we derive approximate analytical results for the optimal investment fractions in various settings . | clarity | 0.9978682 | 0712.2771 | 1 |
We show that , when returns and volatilities of the assets are small and borrowing is forbidden , the Kelly-optimal portfolio lies on Markowitz Efficient Frontier. | <meaning-changed> We show that , when returns and volatilities of the assets are small and borrowing is forbidden , the Kelly-optimal portfolio lies on Markowitz Efficient Frontier. | We show that when mean returns and volatilities of the assets are small and borrowing is forbidden , the Kelly-optimal portfolio lies on Markowitz Efficient Frontier. | meaning-changed | 0.99600226 | 0712.2771 | 1 |
We show that , when returns and volatilities of the assets are small and borrowing is forbidden , the Kelly-optimal portfolio lies on Markowitz Efficient Frontier. | <meaning-changed> We show that , when returns and volatilities of the assets are small and borrowing is forbidden , the Kelly-optimal portfolio lies on Markowitz Efficient Frontier. | We show that , when returns and volatilities of the assets are small and there is no risk-free asset , the Kelly-optimal portfolio lies on Markowitz Efficient Frontier. | meaning-changed | 0.5924381 | 0712.2771 | 1 |
When short positions are also forbidden, only a small fraction of the available assets is included in the Kelly-optimal portfolio. | <meaning-changed> When short positions are also forbidden, only a small fraction of the available assets is included in the Kelly-optimal portfolio. | Since in the investigated case the Kelly approach forbids short positions and borrowing, often only a small fraction of the available assets is included in the Kelly-optimal portfolio. | meaning-changed | 0.99943286 | 0712.2771 | 1 |
Database replication is difficult but indispensable. We report on our experiences building and deploying middleware-based replication systems both as commercial products and research systems. We identify gaps that still separate academic research from industrial practiceand thus thwart potential technology transfer from academia to the field. We structure our analysis along three axes -- performance, availability and management -- and outline unmet database replication challenges at several levels. | <clarity> Database replication is difficult but indispensable. We report on our experiences building and deploying middleware-based replication systems both as commercial products and research systems. We identify gaps that still separate academic research from industrial practiceand thus thwart potential technology transfer from academia to the field. We structure our analysis along three axes -- performance, availability and management -- and outline unmet database replication challenges at several levels. | The need for high availability and performance in data management systems has been fueling a long running interest in database replication from both academia and industry. However, academic groups often attack replication problems in isolation, overlooking the need for completeness in their solutions, while commercial teams take a holistic approach that often misses opportunities for fundamental innovation. This has created over time a gap between academic research and industrial practice. This paper aims to characterize the gap along three axes -- performance, availability and management -- and outline unmet database replication challenges at several levels. | clarity | 0.81634384 | 0712.2773 | 1 |
We structure our analysis along three axes -- performance, availability and management -- and outline unmet database replication challenges at several levels. | <fluency> We structure our analysis along three axes -- performance, availability and management -- and outline unmet database replication challenges at several levels. | We structure our analysis along three axes : performance, availability and management -- and outline unmet database replication challenges at several levels. | fluency | 0.9993761 | 0712.2773 | 1 |
We structure our analysis along three axes -- performance, availability and management -- and outline unmet database replication challenges at several levels. We hope to both motivate and aid researchers in bridging these gaps between theory and practice . | <clarity> We structure our analysis along three axes -- performance, availability and management -- and outline unmet database replication challenges at several levels. We hope to both motivate and aid researchers in bridging these gaps between theory and practice . | We structure our analysis along three axes -- performance, availability , and administration. We build on our own experience developing and deploying replication systems in commercial and academic settings, as well as on a large body of prior related work . | clarity | 0.90432554 | 0712.2773 | 1 |
We sift through the last decade of open-source, academic, and commercial database replication systems and combine this material with case studies resulting from developing and deploying real systems at many customer sites . | <clarity> We sift through the last decade of open-source, academic, and commercial database replication systems and combine this material with case studies resulting from developing and deploying real systems at many customer sites . | We sift through representative examples from the last decade of open-source, academic, and commercial database replication systems and combine this material with case studies resulting from developing and deploying real systems at many customer sites . | clarity | 0.56182337 | 0712.2773 | 1 |
We sift through the last decade of open-source, academic, and commercial database replication systems and combine this material with case studies resulting from developing and deploying real systems at many customer sites . | <clarity> We sift through the last decade of open-source, academic, and commercial database replication systems and combine this material with case studies resulting from developing and deploying real systems at many customer sites . | We sift through the last decade of open-source, academic, and commercial database replication systems and combine this material with case studies from real systems deployed at Fortune 500 customers . | clarity | 0.9412017 | 0712.2773 | 1 |
We propose two agendas, one for academic research and one for industrial R&D, which we expect can bridge the gaps within 5-10 years . | <clarity> We propose two agendas, one for academic research and one for industrial R&D, which we expect can bridge the gaps within 5-10 years . | We propose two agendas, one for academic research and one for industrial R&D, which we believe can bridge the gaps within 5-10 years . | clarity | 0.998018 | 0712.2773 | 1 |
We propose two agendas, one for academic research and one for industrial R&D, which we expect can bridge the gaps within 5-10 years . | <fluency> We propose two agendas, one for academic research and one for industrial R&D, which we expect can bridge the gaps within 5-10 years . | We propose two agendas, one for academic research and one for industrial R&D, which we expect can bridge the gap within 5-10 years . | fluency | 0.9986041 | 0712.2773 | 1 |
We propose two agendas, one for academic research and one for industrial R&D, which we expect can bridge the gaps within 5-10 years . | <meaning-changed> We propose two agendas, one for academic research and one for industrial R&D, which we expect can bridge the gaps within 5-10 years . | We propose two agendas, one for academic research and one for industrial R&D, which we expect can bridge the gaps within 5-10 years . This way, we hope to both motivate and help researchers in making the theory and practice of middleware-based database replication more relevant to each other . | meaning-changed | 0.9989973 | 0712.2773 | 1 |
Using Malliavin calculus techniques, we derive an analytical formula for the price of European options, for any model including local volatility and jump Poisson process. | <fluency> Using Malliavin calculus techniques, we derive an analytical formula for the price of European options, for any model including local volatility and jump Poisson process. | Using Malliavin calculus techniques, we derive an analytical formula for the price of European options, for any model including local volatility and Poisson jump process. | fluency | 0.99864763 | 0712.3485 | 1 |
We show that the accuracy of the formula depends on the smoothness of the payoff . | <clarity> We show that the accuracy of the formula depends on the smoothness of the payoff . | We show that the accuracy of the formula depends on the smoothness of the payoff function . | clarity | 0.9855797 | 0712.3485 | 1 |
Our approach relies on an asymptotic expansion related to small diffusion and small jump frequency . As a consequence, the calibration of such model becomes very fast . | <meaning-changed> Our approach relies on an asymptotic expansion related to small diffusion and small jump frequency . As a consequence, the calibration of such model becomes very fast . | Our approach relies on an asymptotic expansion related to small diffusion and small jump frequency /size. Our formula has excellent accuracy (the error on implied Black-Scholes volatilities for call option is smaller than 2 bp for various strikes and maturities). Additionally, model calibration becomes very rapid . | meaning-changed | 0.99955684 | 0712.3485 | 1 |