wanyu/IteraTeR_full_sent huggingface dataset:
Original:  Then, through nonlinear dynamical analysis we demonstrate that the yeast cell-cycle process is an excited system driven by a sequence of saddle-node bifurcations with ghost effects , and the yeast cell-cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell-cycle checkpoints.
Revised:  Then, through nonlinear dynamic analysis, we demonstrate that the yeast cell-cycle process is an excited system driven by a sequence of saddle-node bifurcations with ghost effects , and the yeast cell-cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell-cycle checkpoints.
Edit intent: clarity
Original:  Then, through nonlinear dynamical analysis we demonstrate that the yeast cell-cycle process is an excited system driven by a sequence of saddle-node bifurcations with ghost effects , and the yeast cell-cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell-cycle checkpoints.
Revised:  Then, through nonlinear dynamical analysis we demonstrate that the yeast cell cycle process is an excited system driven by a sequence of saddle-node bifurcations with ghost effects , and the yeast cell-cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell-cycle checkpoints.
Edit intent: fluency
Original:  Then, through nonlinear dynamical analysis we demonstrate that the yeast cell-cycle process is an excited system driven by a sequence of saddle-node bifurcations with ghost effects , and the yeast cell-cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell-cycle checkpoints.
Revised:  Then, through nonlinear dynamical analysis we demonstrate that the yeast cell-cycle process is an excitable system driven by a sequence of saddle-node bifurcations with ghost effects , and the yeast cell-cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell-cycle checkpoints.
Edit intent: fluency
Original:  Then, through nonlinear dynamical analysis we demonstrate that the yeast cell-cycle process is an excited system driven by a sequence of saddle-node bifurcations with ghost effects , and the yeast cell-cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell-cycle checkpoints.
Revised:  Then, through nonlinear dynamical analysis we demonstrate that the yeast cell-cycle process is an excited system driven by a sequence of saddle-node bifurcations with ghost effects . We further show that the yeast cell cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell-cycle checkpoints.
Edit intent: clarity
Original:  Then, through nonlinear dynamical analysis we demonstrate that the yeast cell-cycle process is an excited system driven by a sequence of saddle-node bifurcations with ghost effects , and the yeast cell-cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell-cycle checkpoints.
Revised:  Then, through nonlinear dynamical analysis we demonstrate that the yeast cell-cycle process is an excited system driven by a sequence of saddle-node bifurcations with ghost effects , and the yeast cell-cycle trajectory is globally attractive with modularity in both state and parameter space, while the convergent manifold provides a suitable control state for cell cycle checkpoints.
Edit intent: fluency
Original: The uniform sampling of convex polytopes is an interesting computational problem with many applications , in particular in the field of metabolic network analysis , but the performances of sampling algorithms can be affected by high condition numbers in real instances .
Revised: The uniform sampling of convex polytopes is an interesting computational problem with many applications , in particular in the field of metabolic network analysis , but the performances of sampling algorithms can be affected by ill-conditioning. This is the case of inferring the feasible steady states in models of metabolic networks, since they can show heterogeneous timescales .
Edit intent: meaning-changed
Original:  In this work we define a procedure in order to reduce the condition number based on building an ellipsoid that closely matches the sampling space . This defines an affine transformation that renders the space homogeneous and suited to an efficient sampling by means of an Hit-and-Run Montecarlo markov chain .
Revised:  In this work we define a procedure in order to reduce the condition number based on building an ellipsoid that closely matches the sampling space , that can be used to define an efficient Hit-and-Run Montecarlo markov chain .
Edit intent: coherence
Original:  We propose two methods in order to build the ellipsoid: one based on principal component analysis and the other on linear programming . We show its performances on highly heterogeneous hyper-rectangles and apply it to a model of the metabolism of the bacterium E.Coli .
Revised:  We propose two methods in order to build the ellipsoid: one based on principal component analysis and the other on linear programming (LP) and finally we employ the Lovazs ellipsoid method (LEM). Our results show that a rounding procedure is mandatory for such inference problems and suggest that a combination of LEM or LP with a subsequent PCA seems to perform the best .
Edit intent: meaning-changed
Original:  In this work we focus on rounding procedures based on building an ellipsoid that closely matches the sampling space, that can be used to define an efficient Hit-and-Run markov chain Monte Carlo.
Revised:  In this work we focus on rounding procedures based on building an ellipsoid that closely matches the sampling space, that can be used to define an efficient hit-and-run (HR) Markov Chain Monte Carlo.
Edit intent: meaning-changed
Original:  Our results show that a rounding procedure is mandatory for such inference problems and suggest that a combination of LEM or LP with a subsequent PCA seems to perform the best  .
Revised:  Our results show that a rounding procedure is mandatory for such inference problems and suggest that a combination of LEM or LP with a subsequent PCA seems to perform the best . We finally compare the distributions of the HR with that of two heuristics based on the Artificially Centered hit-and-run (ACHR), gpSampler and optGpSampler. They show a good agreement with the results of the HR for the small network, while on genome scale models present inconsistencies .
Edit intent: meaning-changed
Original:  Spines used probability coding of Ca2+ increases rather than amplitude coding for input timing detection via stochastic facilitation by utilizing the small number of molecules in a spine volume, which appeared optimalfor probability coding . Probability coding of Ca2+ increases in a spine volume was more robust against input fluctuation and more sensitive to input numbers than amplitude coding of Ca2+ increases in a cell volume.
Revised:  Spines used probability coding of Ca^{2+ increases rather than amplitude coding for input timing detection via stochastic facilitation by utilizing the small number of molecules in a spine volume, which appeared optimalfor probability coding . Probability coding of Ca2+ increases in a spine volume was more robust against input fluctuation and more sensitive to input numbers than amplitude coding of Ca2+ increases in a cell volume.
Edit intent: fluency
Original:  Spines used probability coding of Ca2+ increases rather than amplitude coding for input timing detection via stochastic facilitation by utilizing the small number of molecules in a spine volume, which appeared optimalfor probability coding . Probability coding of Ca2+ increases in a spine volume was more robust against input fluctuation and more sensitive to input numbers than amplitude coding of Ca2+ increases in a cell volume.
Revised:  Spines used probability coding of Ca2+ increases rather than amplitude coding for input timing detection via stochastic facilitation by utilizing the small number of molecules in a spine volume, where information per volume appeared optimal . Probability coding of Ca2+ increases in a spine volume was more robust against input fluctuation and more sensitive to input numbers than amplitude coding of Ca2+ increases in a cell volume.
Edit intent: clarity
Original:  Spines used probability coding of Ca2+ increases rather than amplitude coding for input timing detection via stochastic facilitation by utilizing the small number of molecules in a spine volume, which appeared optimalfor probability coding . Probability coding of Ca2+ increases in a spine volume was more robust against input fluctuation and more sensitive to input numbers than amplitude coding of Ca2+ increases in a cell volume.
Revised:  Spines used probability coding of Ca2+ increases rather than amplitude coding for input timing detection via stochastic facilitation by utilizing the small number of molecules in a spine volume, which appeared optimalfor probability coding . Probability coding of Ca^{2+ increases in a spine volume was more robust against input fluctuation and more sensitive to input numbers than amplitude coding of Ca2+ increases in a cell volume.
Edit intent: fluency
Original:  Spines used probability coding of Ca2+ increases rather than amplitude coding for input timing detection via stochastic facilitation by utilizing the small number of molecules in a spine volume, which appeared optimalfor probability coding . Probability coding of Ca2+ increases in a spine volume was more robust against input fluctuation and more sensitive to input numbers than amplitude coding of Ca2+ increases in a cell volume.
Revised:  Spines used probability coding of Ca2+ increases rather than amplitude coding for input timing detection via stochastic facilitation by utilizing the small number of molecules in a spine volume, which appeared optimalfor probability coding . Probability coding of Ca2+ increases in a spine volume was more robust against input fluctuation and more sensitive to input numbers than amplitude coding of Ca^{2+ increases in a cell volume.
Edit intent: fluency
Original: In quantitative finance, we often wish to recover the volatility of asset prices given by a noisy It\=o semimartingale. Existing estimates, however, lose accuracy when the jumps are of infinite variation, as is suggested by empirical evidence .
Revised: In quantitative finance, we often wish to recover the volatility of asset prices given by a noisy Ito semimartingale; unfortunately, this model is too complex to identify from price data .
Edit intent: meaning-changed
Original:  In this paper, we show that when the efficient prices are given by an unknown time-changed L\'evy process, the rate of time change, which plays the role of the volatility, can be estimated well under arbitrary jump activity.
Revised:  In this paper, we therefore consider efficient prices given by a time-changed L\'evy process, the rate of time change, which plays the role of the volatility, can be estimated well under arbitrary jump activity.
Edit intent: clarity
Original:  In this paper, we show that when the efficient prices are given by an unknown time-changed L\'evy process, the rate of time change, which plays the role of the volatility, can be estimated well under arbitrary jump activity.
Revised:  In this paper, we show that when the efficient prices are given by an unknown time-changed Levy process; this model is both identifiable, and replicates salient features of price data. We give a new estimate of the rate process in this model, which governs its volatility. Our estimate obtains minimax convergence rates, and is unaffected by arbitrary jump activity.
Edit intent: meaning-changed
Original:  Our estimate obtains minimax convergence rates, and is unaffected by arbitrary jump activity. Furthermore, it remains valid for the volatility in the general semimartingale model , obtaining convergence rates as good as any previously implied in the literature.
Revised:  Our estimate obtains minimax convergence rates, and is unaffected by infinite-variation jumps. In the semimartingale model, our estimate remains accurate for the normalised volatility , obtaining convergence rates as good as any previously implied in the literature.
Edit intent: clarity
Original:  By linking single-cell experiments on the lactose-uptake pathway in E. coli to molecular simulations, we devise a general method to pinpoint the particular fluctuation driving phenotype switching and apply it to the transition between the uninduced and induced states of the lac-genes .
Revised:  By linking single-cell experiments on the lactose-uptake pathway in E. coli to molecular simulations, we devise a general method to pinpoint the particular fluctuation driving phenotype switching and apply this method to the transition between the uninduced and induced states of the lac-genes .
Edit intent: clarity
Original:  By linking single-cell experiments on the lactose-uptake pathway in E. coli to molecular simulations, we devise a general method to pinpoint the particular fluctuation driving phenotype switching and apply it to the transition between the uninduced and induced states of the lac-genes .
Revised:  By linking single-cell experiments on the lactose-uptake pathway in E. coli to molecular simulations, we devise a general method to pinpoint the particular fluctuation driving phenotype switching and apply it to the transition between the uninduced and induced states of the lac genes .
Edit intent: fluency
Original: Cells with identical genomes often exhibit biochemically distinct phenotypic states ; stochastic switchings among them are one of the functional roles of "noise" in a genetic circuitry. To quantify the stabilities of these phenotypic states and, more importantly, the transition rates among them, we study a minimal model of gene regulation that incorporates positive feedbackwith multiple gene states. We first show that starting from a full Delbr\"uck-Gillespie-process description of the gene regulation network, two much simpler stochastic biochemical kinetic systems can be deduced, respectively, in the limit of either the stochastic gene-state switching or transcription factor copy-number fluctuation being dominant among other sources of noise.
Revised: Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can be neither extremely slow nor exceedingly rapid as many previous theoretical treatments assumed. Rather it is in the intermediate region which is difficult to handle mathematically.Under this condition, from a full Delbr\"uck-Gillespie-process description of the gene regulation network, two much simpler stochastic biochemical kinetic systems can be deduced, respectively, in the limit of either the stochastic gene-state switching or transcription factor copy-number fluctuation being dominant among other sources of noise.
Edit intent: meaning-changed
Original:  We first show that starting from a full Delbr\"uck-Gillespie-process description of the gene regulation network, two much simpler stochastic biochemical kinetic systems can be deduced, respectively, in the limit of either the stochastic gene-state switching or transcription factor copy-number fluctuation being dominant among other sources of noise.
Revised:  We first show that starting from a full chemical-master-equation description we derive a model in which the protein copy-number, for a given gene state, follow a deterministic mean-field description while the protein synthesis rates fluctuate due to stochastic gene-state switching or transcription factor copy-number fluctuation being dominant among other sources of noise.
Edit intent: meaning-changed
Original:  We first show that starting from a full Delbr\"uck-Gillespie-process description of the gene regulation network, two much simpler stochastic biochemical kinetic systems can be deduced, respectively, in the limit of either the stochastic gene-state switching or transcription factor copy-number fluctuation being dominant among other sources of noise. We then propose two saddle-crossing rate formulas for the simplified dynamics. They are associated with the barriers of different nonequilibrium landscape functions, whichexhibit different dependence on the switching rates of gene states. Keeping exactly the same mean-field deterministic dynamics, incorporating noise can possibly yield opposite predictions on the relative stability of the coexisted phenotypic states when the single-molecule switching between different gene states, compared to the protein copy-number fluctuation, is relatively slow or sufficiently rapid. This quantitative theory emphasizes noises from different origins with distinct characteristics as an additional complexity within gene regulation .
Revised:  We first show that starting from a full Delbr\"uck-Gillespie-process description of the gene regulation network, two much simpler stochastic biochemical kinetic systems can be deduced, respectively, in the limit of either the stochastic gene-state switching . The simplified kinetics yields a nonequilibrium landscape function, which, similar to the energy function for equilibrium fluctuation, provides the leading orders of fluctuations around each phenotypic state, as well as the transition rates between the two phenotypic states. This rate formula is analogous to Kramers theory for chemical reactions. The resulting behaviors are significantly different from the two limiting cases studied previously .
Edit intent: coherence
Original:  We suggest that many of these 2,001 genes do not code for proteins under normal circumstances and that they should not be included in the human protein coding gene catalogue  .
Revised:  We suggest that many of these 2,001 genes do not code for proteins under normal circumstances and that they should not be included in the human protein coding gene catalogue . These potential non-coding genes will be revised as part of the ongoing human genome annotation effort .
Edit intent: meaning-changed
Original: This paper introduces the notion of public collaborative processes (PCPs)to the field of Business Process Management (BPM) . PCPs involve URLanizations with a common objective, where a number of URLanizations cooperating under various unstructured forms  take a collaborative approach to reaching the final goal.
Revised: The 2007--2008 financial crisis has paved the way for the use of macroprudential policies in supervising the financial system as a whole. This paper views macroprudential oversight in Europe as a process, a sequence of activities with the ultimate aim of safeguarding financial stability. To conceptualize a process in this context, we introduce the notion of a public collaborative process (PCP) . PCPs involve URLanizations with a common objective, where a number of URLanizations cooperating under various unstructured forms take a collaborative approach to reaching the final goal.
Edit intent: meaning-changed
Original: This paper introduces the notion of public collaborative processes (PCPs)to the field of Business Process Management (BPM) . PCPs involve URLanizations with a common objective, where a number of URLanizations cooperating under various unstructured forms  take a collaborative approach to reaching the final goal.
Revised: This paper introduces the notion of public collaborative processes (PCPs)to the field of Business Process Management (BPM) . PCPs involve URLanizations with a common objective, where a number of URLanizations cooperate under various unstructured forms take a collaborative approach to reaching the final goal.
Edit intent: fluency
Original: This paper introduces the notion of public collaborative processes (PCPs)to the field of Business Process Management (BPM) . PCPs involve URLanizations with a common objective, where a number of URLanizations cooperating under various unstructured forms  take a collaborative approach to reaching the final goal.
Revised: This paper introduces the notion of public collaborative processes (PCPs)to the field of Business Process Management (BPM) . PCPs involve URLanizations with a common objective, where a number of URLanizations cooperating under various unstructured forms and take a collaborative approach to reaching the final goal.
Edit intent: coherence
Original:  This paper exemplifies the analysis of PCPs with the case of safeguarding financial stability, particularly macroprudential oversight in Europe. Following the literature on BPM, this paper models the macroprudential oversight process as an event-driven process chain, including activities, responsible entities, as well as inputs and outputs. We view the process from two directions. As an initial step, we document a high-level representation of the process (i.e., without specifying responsible entities) as depicted in the literature. Moreover, we show the increase in complexity when moving to a low-level description of the process (i.e., specifying responsible entities). Along these lines, we put forward a matrix view consisting of five necessary steps to managing PCPs. Thus, in terms of managing the macroprudential oversight process, this motivates further work in collaboration with experts to document, analyze and improve the macroprudential oversight process at a more detailed level .
Revised:  We argue that PCPs can and should essentially be managed using the tools and practices common for business processes. To this end, we conduct an assessment of process readiness for macroprudential oversight in Europe. Based upon interviews with key European policymakers and supervisors, we provide an analysis model to assess the maturity of five process enablers for macroprudential oversight. With the results of our analysis, we give clear recommendations on the areas that need further attention when macroprudential oversight is being developed, in addition to providing a general purpose framework for monitoring the impact of improvement efforts .
Edit intent: coherence
Original: By analysing the financial data of firms across Japan, a non-trivial power law with exponent 1.3 is observed between the number of business partners (i.e. the degree of the inter-firm trading network) and sales.
Revised: By analysing the financial data of firms across Japan, a nonlinear power law with exponent 1.3 is observed between the number of business partners (i.e. the degree of the inter-firm trading network) and sales.
Edit intent: clarity
Original: By analysing the financial data of firms across Japan, a non-trivial power law with exponent 1.3 is observed between the number of business partners (i.e. the degree of the inter-firm trading network) and sales.
Revised: By analysing the financial data of firms across Japan, a non-trivial power law with an exponent of 1.3 is observed between the number of business partners (i.e. the degree of the inter-firm trading network) and sales.
Edit intent: clarity
Original: By analysing the financial data of firms across Japan, a non-trivial power law with exponent 1.3 is observed between the number of business partners (i.e. the degree of the inter-firm trading network) and sales.
Revised: By analysing the financial data of firms across Japan, a non-trivial power law with exponent 1.3 was observed between the number of business partners (i.e. the degree of the inter-firm trading network) and sales.
Edit intent: fluency