wanyu/IteraTeR_full_sent huggingface dataset:
Original:  More importantly , the model allows to pinpoint few deviations in human from the neutral scenario it assumes: three over-expanded families corresponding to HOX and FOX type genes , a set of "singleton" TFs for which duplication seems to be selected against, and an higher-than-average rate of diversification of the binding preferences of TFs with a Zinc Finger DNA binding domain.
Revised:  More importantly , the model allows to pinpoint few deviations in human from the neutral scenario it assumes: three over-expanded families corresponding to HOX and FOX type genes , a set of "singleton" TFs for which duplication seems to be selected against, and a higher-than-average rate of diversification of the binding preferences of TFs with a Zinc Finger DNA binding domain.
Edit intent: fluency
Original: We generalize the fundamental theorem of asset pricing (FTAP) and hedging dualities in \mbox{%DIFAUXCMD ZZ8 the case where the investor can  short American options.
Revised: Since most of the traded options on individual stocks is of American type it is of interest to generalize the results obtained in semi-static trading to the case when one is allowed to statically trade American options. However, this problem has proved to be elusive so far because of the asymmetric nature of the positions of holding versus shorting such options. Here we provide a unified framework and generalize the fundamental theorem of asset pricing (FTAP) and hedging dualities in \mbox{%DIFAUXCMD ZZ8 the case where the investor can short American options.
Edit intent: meaning-changed
Original: We generalize the fundamental theorem of asset pricing (FTAP) and hedging dualities in \mbox{%DIFAUXCMD ZZ8 the case where the investor can  short American options.
Revised: We generalize the fundamental theorem of asset pricing (FTAP) and hedging dualities in arXiv:1502.06681 (to appear in Annals of Applied Probability) to the case where the investor can short American options.
Edit intent: meaning-changed
Original: We generalize the fundamental theorem of asset pricing (FTAP) and hedging dualities in \mbox{%DIFAUXCMD ZZ8 the case where the investor can  short American options.
Revised: We generalize the fundamental theorem of asset pricing (FTAP) and hedging dualities in \mbox{%DIFAUXCMD ZZ8 the case where the investor can also short American options.
Edit intent: meaning-changed
Original: We present numerical simulations of active fluid droplets immersed in an external fluid in 2-dimensions . We use an Immersed Boundary method to simulate the fluid droplet interface as a Lagrangian mesh.
Revised: We present numerical simulations of active fluid droplets immersed in an external fluid in 2-dimensions using an Immersed Boundary method to simulate the fluid droplet interface as a Lagrangian mesh.
Edit intent: fluency
Original:  We present results from two example systems, firstly a droplet filled with an active polar fluid with polar anchoring at the droplet interface. Secondly, an active isotropic fluid consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility  }  . These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom.
Revised:  We present results from two example systems, firstly an active isotropic fluid boundary consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility } . These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom.
Edit intent: clarity
Original:  Secondly, an active isotropic fluid consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility  }  . These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom.
Revised:  Secondly, an active isotropic fluid consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility . Secondly, a droplet filled with an active polar fluid with } . These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom.
Edit intent: meaning-changed
Original:  Secondly, an active isotropic fluid consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility  }  . These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom.
Revised:  Secondly, an active isotropic fluid consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility homeotropic} . These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom.
Edit intent: meaning-changed
Original:  Secondly, an active isotropic fluid consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility  }  . These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom.
Revised:  Secondly, an active isotropic fluid consisting of particles that can bind and unbind from the interface and generate surface tension gradients through active contractility } anchoring at the droplet interface . These two systems demonstrate spontaneous symmetry breaking and steady state dynamics resembling cell motility and division and show complex feedback mechanisms with minimal degrees of freedom.
Edit intent: meaning-changed
Original:  We present a  framework for the construction and analysis of metabolic reaction networksthat can be tailored to reflect different environmental conditions . Using context-dependent flux distributions from Flux Balance Analysis (FBA), we produce directed networks with weighted links representing the amount of metabolite flowing from a source reaction to a target reaction per unit time.
Revised:  We present a systematic flux-based framework for the construction and analysis of metabolic reaction networksthat can be tailored to reflect different environmental conditions . Using context-dependent flux distributions from Flux Balance Analysis (FBA), we produce directed networks with weighted links representing the amount of metabolite flowing from a source reaction to a target reaction per unit time.
Edit intent: meaning-changed
Original:  We present a  framework for the construction and analysis of metabolic reaction networksthat can be tailored to reflect different environmental conditions . Using context-dependent flux distributions from Flux Balance Analysis (FBA), we produce directed networks with weighted links representing the amount of metabolite flowing from a source reaction to a target reaction per unit time.
Revised:  We present a framework for the construction of graphs to URLanism-wide metabolic networks. Our graphs encode the directionality of metabolic fluxes via links that represent the flow of metabolites from source to target reactions. The methodology can be applied in the absence of a specific biological context by modelling fluxes as probabilities, or tailored to different environmental conditions . Using context-dependent flux distributions from Flux Balance Analysis (FBA), we produce directed networks with weighted links representing the amount of metabolite flowing from a source reaction to a target reaction per unit time.
Edit intent: meaning-changed
Original:  We present a  framework for the construction and analysis of metabolic reaction networksthat can be tailored to reflect different environmental conditions . Using context-dependent flux distributions from Flux Balance Analysis (FBA), we produce directed networks with weighted links representing the amount of metabolite flowing from a source reaction to a target reaction per unit time.
Revised:  We present a framework for the construction and analysis of metabolic reaction networksthat can be tailored to reflect different environmental conditions by incorporating flux distributions computed from constraint-based modelling such as Flux Balance Analysis (FBA), we produce directed networks with weighted links representing the amount of metabolite flowing from a source reaction to a target reaction per unit time.
Edit intent: meaning-changed
Original:  We present a  framework for the construction and analysis of metabolic reaction networksthat can be tailored to reflect different environmental conditions . Using context-dependent flux distributions from Flux Balance Analysis (FBA), we produce directed networks with weighted links representing the amount of metabolite flowing from a source reaction to a target reaction per unit time. Such networks are analyzed with tools from network theory to reveal salient features of metabolite flows in each biological context.
Revised:  We present a framework for the construction and analysis of metabolic reaction networksthat can be tailored to reflect different environmental conditions . Using context-dependent flux distributions from Flux Balance Analysis .
Edit intent: clarity
Original:  We illustrate our approach with the directed network of the central carbon metabolism of Escherichia coli , and study its properties in four relevant biological scenarios. Our results show that both flow and network structure depend drastically on the environment: networks produced from the same metabolic model in different contexts have different edges, components, and flow communities, capturing the biological re-routing of metabolic flows inside the cell .
Revised:  We illustrate our approach with the directed network of the central carbon metabolism of Escherichia coli and study the derived graphs under various growth conditions. The results reveal drastic changes in the topological and community structure of the metabolic graphs, which capture the re-routing of metabolic flows inside the cell .
Edit intent: clarity
Original:  Our results show that both flow and network structure depend drastically on the environment: networks produced from the same metabolic model in different contexts have different edges, components, and flow communities, capturing the biological re-routing of metabolic flows inside the cell .
Revised:  Our results show that both flow and network structure depend drastically on the environment: networks produced from the same metabolic model in different contexts have different edges, components, and flow communities, capturing the biological re-routing of metabolic fluxes under each growth condition .
Edit intent: clarity
Original:  The methodology can be applied in the absence of a specific biological context by modelling fluxes as probabilities, or tailored to different environmental conditions by incorporating flux distributions computed from constraint-based modelling such as Flux Balance Analysis.
Revised:  The methodology can be applied in the absence of a specific biological context by modelling fluxes probabilistically, or can be tailored to different environmental conditions by incorporating flux distributions computed from constraint-based modelling such as Flux Balance Analysis.
Edit intent: clarity
Original:  The methodology can be applied in the absence of a specific biological context by modelling fluxes probabilistically, or can be tailored to different environmental conditions by incorporating flux distributions computed from constraint-based modelling such as Flux Balance Analysis.
Revised:  The methodology can be applied in the absence of a specific biological context by modelling fluxes probabilistically, or can be tailored to different environmental conditions by incorporating flux distributions computed through constraint-based modelling such as Flux Balance Analysis.
Edit intent: clarity
Original:  The methodology can be applied in the absence of a specific biological context by modelling fluxes probabilistically, or can be tailored to different environmental conditions by incorporating flux distributions computed from constraint-based modelling such as Flux Balance Analysis.
Revised:  The methodology can be applied in the absence of a specific biological context by modelling fluxes probabilistically, or can be tailored to different environmental conditions by incorporating flux distributions computed from constraint-based approaches such as Flux Balance Analysis.
Edit intent: clarity
Original:  We illustrate our approach on the central carbon metabolism of Escherichia coli , and on a larger metabolic model of human hepatocytes , and study the proposed graphs under various environmental conditions and genetic perturbations .
Revised:  We illustrate our approach on the central carbon metabolism of Escherichia coli and on a larger metabolic model of human hepatocytes , and study the proposed graphs under various environmental conditions and genetic perturbations .
Edit intent: fluency
Original:  We illustrate our approach on the central carbon metabolism of Escherichia coli , and on a larger metabolic model of human hepatocytes , and study the proposed graphs under various environmental conditions and genetic perturbations .
Revised:  We illustrate our approach on the central carbon metabolism of Escherichia coli , and on a metabolic model of human hepatocytes , and study the proposed graphs under various environmental conditions and genetic perturbations .
Edit intent: clarity
Original:  We illustrate our approach on the central carbon metabolism of Escherichia coli , and on a larger metabolic model of human hepatocytes , and study the proposed graphs under various environmental conditions and genetic perturbations .
Revised:  We illustrate our approach on the central carbon metabolism of Escherichia coli , and on a larger metabolic model of human hepatocytes . The flux-dependent graphs under various environmental conditions and genetic perturbations .
Edit intent: meaning-changed
Original:  We illustrate our approach on the central carbon metabolism of Escherichia coli , and on a larger metabolic model of human hepatocytes , and study the proposed graphs under various environmental conditions and genetic perturbations . The results reveal drastic changes in the topological and community structure of the metabolic graphs , which capture the re-routing of metabolic fluxes under each growth and genetic condition .
Revised:  We illustrate our approach on the central carbon metabolism of Escherichia coli , and on a larger metabolic model of human hepatocytes , and study the proposed graphs under various environmental conditions and genetic perturbations exhibit systemic changes in their topological and community structure of the metabolic graphs , which capture the re-routing of metabolic fluxes under each growth and genetic condition .
Edit intent: clarity
Original:  We use results of Hou \& Ob\l\'oj \mbox{%DIFAUXCMD ho_beliefs on robust approach with beliefs to establish the pricing--hedging duality for an informed agent.
Revised:  We use results of Hou Ob\l\'oj \mbox{%DIFAUXCMD ho_beliefs on robust approach with beliefs to establish the pricing--hedging duality for an informed agent.
Edit intent: fluency
Original:  When gradients are shallow or noisy, URLanisms move by alternating straight motion (runs) with random reorientations (tumbles) . Navigation is achieved by transiently reducing the probability to tumble when attractant signal increases.
Revised:  When gradients are shallow or noisy, URLanisms move by alternating straight motion (runs) with random reorientations (tumbles) , transiently suppressing tumbles whenever attractant signal increases.
Edit intent: clarity
Original:  One drawback of this strategy is that occasional runs in the wrong direction reduce progress up the gradient. Here we discovered a positive feedback regime inherent in this strategy that strongly mitigates this problem. In an attractant field, motion up the gradient reduces tumble probability, which further boosts drift up the gradient.
Revised:  This induces a functional coupling between movement and sensation, since tumbling probability is controlled by the internal state of URLanism which, in turn, depends on previous signal levels. Although a negative feedback tends to maintain this internal state close to adapted levels, positive feedback can arise when motion up the gradient reduces tumble probability, which further boosts drift up the gradient.
Edit intent: meaning-changed
Original:  This positive feedback can drive large fluctuations in the internal state of URLanism away from its mean, resulting in long runs in favorable directions but short ones otherwise.
Revised:  This positive feedback can drive large fluctuations in the internal state , complicating analytical approaches. Previous studies focused on what happens when the negative feedback dominates the dynamics. By contrast, we show here that there is a large portion of physiologically-relevant parameter space where the positive feedback can dominate, even when gradients are relatively shallow. We demonstrate how large transients emerge because of non-normal dynamics (non-orthogonal eigenvectors near a stable fixed point) inherent in the positive feedback, and further identify a fundamental nonlinearity that strongly amplifies their effect. Most importantly, this amplification is asymmetric, elongating runs in favorable directions but short ones otherwise.
Edit intent: meaning-changed
Original:  This positive feedback can drive large fluctuations in the internal state of URLanism away from its mean, resulting in long runs in favorable directions but short ones otherwise. In this new regime URLanism achieves a "ratchet-like" gradient climbing behavior unexpected from mean field theory, and drift speeds much faster than previously believed possible .
Revised:  This positive feedback can drive large fluctuations in the internal state of URLanism away from its mean, resulting in long runs in favorable directions and abbreviating others. The result is a "ratchet-like" gradient climbing behavior unexpected from mean field theory, and drift speeds much faster than previously believed possible .
Edit intent: clarity
Original:  In this new regime URLanism achieves a "ratchet-like" gradient climbing behavior unexpected from mean field theory, and drift speeds much faster than previously believed possible .
Revised:  In this new regime URLanism achieves a "ratchet-like" gradient climbing behavior with drift speeds that can approach half the maximum run speed of URLanism. Our results thus show that the classical drawback of run-and-tumble navigation --- wasteful runs in the wrong direction --- can be mitigated by exploiting the non-normal dynamics implicit in the run-and-tumble strategy .
Edit intent: meaning-changed
Original:  It is known that gradient maps of exponentially concave functions are solutions of a Monge-Kantorovich optimal transport problem and allow for a better gradient approximation than those of ordinary concave functions.
Revised:  In a previous paper we showed that gradient maps of exponentially concave functions are solutions of a Monge-Kantorovich optimal transport problem and allow for a better gradient approximation than those of ordinary concave functions.
Edit intent: meaning-changed
Original:  Using the tools of information geometry and optimal transport, we show that L-divergence induces a new information geometry on the simplex . This geometric structure consists of a Riemannian metric and a pair of dually coupled affine connections defining two kinds of geodesics.
Revised:  Using the tools of information geometry and optimal transport, we show that L-divergence induces a new information geometry on the simplex consisting of a Riemannian metric and a pair of dually coupled affine connections defining two kinds of geodesics.
Edit intent: clarity
Original:  We previously speculated that the mechanism of DNA to DNA transcription might be similar to that of DNA to RNA transcription, but there is another mechanism that we think is most likely to be true. The mechanism is called endonuclease dependent transcript cutout  , in which a copy of ssDNA fragment (transcript) between two nicks produced by nicking endonuclease is released from double-stranded DNA region in the genome by an unknown ssDNA fragment-releasing enzyme.
Revised:  We previously speculated that the mechanism of DNA to DNA transcription might be similar to that of DNA to RNA transcription, but now we propose that endonuclease dependent transcript cutout , in which a copy of ssDNA fragment (transcript) between two nicks produced by nicking endonuclease is released from double-stranded DNA region in the genome by an unknown ssDNA fragment-releasing enzyme.
Edit intent: coherence
Original:  The mechanism is called endonuclease dependent transcript cutout  , in which a copy of ssDNA fragment (transcript) between two nicks produced by nicking endonuclease is released from double-stranded DNA region in the genome by an unknown ssDNA fragment-releasing enzyme.
Revised:  The mechanism is called endonuclease dependent transcript cutout may be a possible mechanism of DNA to DNA transcription , in which a copy of ssDNA fragment (transcript) between two nicks produced by nicking endonuclease is released from double-stranded DNA region in the genome by an unknown ssDNA fragment-releasing enzyme.
Edit intent: meaning-changed
Original:  The mechanism is called endonuclease dependent transcript cutout  , in which a copy of ssDNA fragment (transcript) between two nicks produced by nicking endonuclease is released from double-stranded DNA region in the genome by an unknown ssDNA fragment-releasing enzyme.
Revised:  The mechanism is called endonuclease dependent transcript cutout , in which a copy of ssDNA fragment (transcript) between two nicks produced by nicking endonuclease is released from double-stranded DNA region in the genome by an unknown ssDNA fragment releasing enzyme.
Edit intent: fluency
Original:  We once speculated that the mechanism of DNA to DNA transcription might be similar to that of DNA to RNA transcription, but now we propose that endonuclease dependent transcript cutout may be a possible mechanism of DNA to DNA transcription, in which a copy of ssDNA fragment (transcript) between two nicks produced by nicking endonuclease is released from double-stranded DNA  region in the genome by an unknown ssDNA fragment releasing enzyme.
Revised:  We once speculated that the mechanism of DNA to DNA transcription might be similar to that of DNA to RNA transcription, but now we propose that endonuclease dependent transcript cutout may be a possible mechanism of DNA to DNA transcription, in which a copy of ssDNA fragment (transcript) between two nicks produced by nicking endonuclease is released from double-stranded DNA (dsDNA) region in the genome by an unknown ssDNA fragment releasing enzyme.
Edit intent: clarity