wanyu/IteraTeR_v2 huggingface dataset:
Original:  A master equation previously derived in the adiabatic limit of fast switching by Kepler and Elston 1 is suggested for stochastic gene expression to take into account inter-state switching processes.
Revised:  A master equation previously derived in the adiabatic limit of fast switching by Kepler and Elston 1 \mbox{ kepler processes.
Edit intent: clarity
Original:  The master equation contains an extra term that describes the gene copy number  diffusion and is responsible for the oscillations .
Revised:  The master equation contains an extra term that describes the gene copy number unconventional diffusion and is responsible for the oscillations .
Edit intent: fluency
Original: In recent years, dynamic languages, such as JavaScript or Python, have faced an important increment of usage in a wide range of fields and applications.
Revised: In recent years, dynamic languages, such as JavaScript or Python, have been increasingly used in a wide range of fields and applications.
Edit intent: clarity
Original:  Unfortunately, string analyses for dynamic languages still lack of precision and do not take into account some important string features.
Revised:  Unfortunately, string analyses for dynamic languages still lack precision and do not take into account some important string features.
Edit intent: fluency
Original:  This paper  proposes a new semantics for string analysis  placing a first step for handling dynamic languages string features.
Revised:  This paper proposes a new semantics for string analysis , placing a first step for handling dynamic languages string features.
Edit intent: fluency
Original:  The results indicate that, for typical, empirically observed combinations of the parameters of the evolutionary process, namely, effective population size, mutation rate, and distribution of selection coefficients of mutations, the probability of a multi-mutation leap is low, and accordingly, their contribution to the evolutionary process is minor at best.
Revised:  The results indicate that, for typical, empirically observed combinations of the parameters of the evolutionary process, namely, effective population size, mutation rate, and distribution of selection coefficients of mutations, the probability of a multi-mutation leap is low, and accordingly, the contribution of such leaps is minor at best.
Edit intent: clarity
Original:  However, such leaps could become an important factor of evolution in situations of population bottlenecks and elevated mutation rates, such as stress-induced mutagenesis in microbes or tumor progression, as well as major evolutionary transitions and evolution of primordial replicators .
Revised:  However, such leaps could become an important factor of evolution in cases of substantially elevated mutation rates, such as stress-induced mutagenesis in microbes or tumor progression, as well as major evolutionary transitions and evolution of primordial replicators .
Edit intent: clarity
Original:  Various relaying schemes , namely, cooperative jamming, decode-and-forward, and amplify-and-forward are proposed and analyzed for that matter , in each of which secure beamforming signals are devised at the relays to maximize the achievable secrecy rate regions.
Revised:  Various relaying schemes are proposed and analyzed for that matter , in each of which secure beamforming signals are devised at the relays to maximize the achievable secrecy rate regions.
Edit intent: coherence
Original:  Various relaying schemes , namely, cooperative jamming, decode-and-forward, and amplify-and-forward are proposed and analyzed for that matter , in each of which secure beamforming signals are devised at the relays to maximize the achievable secrecy rate regions.
Revised:  Various relaying schemes , namely, cooperative jamming, decode-and-forward, and amplify-and-forward are proposed and analyzed for that matter : cooperative jamming, decode-and-forward, and amplify-and-forward. For each scheme, secure beamforming signals are devised at the relays to maximize the achievable secrecy rate regions.
Edit intent: clarity
Original:  For the second scenario, with the untrusted relay, achievable secrecy rate regions are derived for two different relaying schemes , namely, compress-and-forward and amplify-and-forward, under two different modes of operation.
Revised:  For the second scenario, with the untrusted relay, achievable secrecy rate regions are derived for two different relaying schemes : compress-and-forward and amplify-and-forward, under two different modes of operation.
Edit intent: coherence
Original:  The results show that the best relaying scheme highly depends on the system parameters, in particular distances between the nodes, and also on which part of the secrecy rate region the system is to operate at.
Revised:  It is shown that the best relaying scheme highly depends on the system parameters, in particular distances between the nodes, and also on which part of the secrecy rate region the system is to operate at.
Edit intent: clarity
Original: Species' densities experience both internal frequency-dependent feedbacks due spatial, age, or genetic structure , and external feedbacks with abiotic factorssuch as climatic conditions and nutrient availability .
Revised: Species' densities experience both internal frequency-dependent feedbacks due to population structure and external feedbacks with abiotic factorssuch as climatic conditions and nutrient availability .
Edit intent: clarity
Original: Species' densities experience both internal frequency-dependent feedbacks due spatial, age, or genetic structure , and external feedbacks with abiotic factorssuch as climatic conditions and nutrient availability .
Revised: Species' densities experience both internal frequency-dependent feedbacks due spatial, age, or genetic structure , and external feedbacks from abiotic factors .
Edit intent: clarity
Original:  These feedbacks play an important role in determining whether populations persist or go extinct  and may be subject to stochastic fluctuations.
Revised:  These feedbacks can determine whether populations persist or go extinct and may be subject to stochastic fluctuations.
Edit intent: clarity
Original:  These feedbacks play an important role in determining whether populations persist or go extinct  and may be subject to stochastic fluctuations.
Revised:  These feedbacks play an important role in determining whether populations persist or go extinct , and may be subject to stochastic fluctuations.
Edit intent: fluency
Original:  We develop theorems for stochastic persistence and exclusion for stochastic ecological difference equations accounting for these feedbacks.
Revised:  We develop theorems for stochastic persistence and exclusion for stochastic ecological difference equations accounting for feedbacks.
Edit intent: fluency
Original:  Specifically, we use the stochastic analog of average Lyapunov functions to develop sufficient and necessary conditions for (i) all population densities to spend little time at low densities , (ii) population trajectories asymptotically approaching the extinction set with positive probability , and (iii) under an additional accessibility condition, this asymptotic extinction occurring with probability one .
Revised:  Specifically, we use the stochastic analog of average Lyapunov functions to develop sufficient and necessary conditions for (i) all population densities spending little time at low densities , (ii) population trajectories asymptotically approaching the extinction set with positive probability , and (iii) under an additional accessibility condition, this asymptotic extinction occurring with probability one .
Edit intent: fluency
Original:  To illustrate our results, we analyze models of (a) trait evolution, (b) spatially structured disease dynamics , (c) competing species, and (d) evolutionary games .
Revised:  To illustrate our results, we analyze models of (a) trait evolution, and spatially structured disease dynamics , (c) competing species, and (d) evolutionary games .
Edit intent: coherence
Original:  To illustrate our results, we analyze models of (a) trait evolution, (b) spatially structured disease dynamics , (c) competing species, and (d) evolutionary games .
Revised:  To illustrate our results, we analyze models of (a) trait evolution, (b) spatially structured disease dynamics .
Edit intent: clarity
Original:  In contrast , environmental fluctuations can promote disease persistence in patchy landscapes (b) . While these results help close the gap between the persistence theories for deterministic and stochastic systems, we conclude by highlighting several challenges for future research.
Revised:  In contrast , environmental fluctuations can promote disease persistence in patchy landscapes . While these results help close the gap between the persistence theories for deterministic and stochastic systems, we conclude by highlighting several challenges for future research.
Edit intent: coherence
Original:  In contrast , environmental fluctuations can promote disease persistence in patchy landscapes (b) . While these results help close the gap between the persistence theories for deterministic and stochastic systems, we conclude by highlighting several challenges for future research.
Revised:  In contrast , environmental fluctuations can promote disease persistence in patchy landscapes (b) . While these results help close the gap between persistence theories for deterministic and stochastic systems, we conclude by highlighting several challenges for future research.
Edit intent: fluency
Original:  To provide a general mathematical framework for studying these effects, we develop theorems for stochastic persistence and exclusion for stochastic ecological difference equations accounting for feedbacks . Specifically, we use the stochastic analog of average Lyapunov functions to develop sufficient and necessary conditions for (i)
Revised:  To provide a general mathematical framework for studying these effects, we develop theorems for stochastic persistence and exclusion for stochastic ecological difference equations accounting for internal and external variables . Specifically, we use the stochastic analog of average Lyapunov functions to develop sufficient and necessary conditions for (i)
Edit intent: clarity
Original:  To provide a general mathematical framework for studying these effects, we develop theorems for stochastic persistence and exclusion for stochastic ecological difference equations accounting for feedbacks . Specifically, we use the stochastic analog of average Lyapunov functions to develop sufficient and necessary conditions for (i)
Revised:  To provide a general mathematical framework for studying these effects, we develop theorems for stochastic persistence and exclusion for stochastic ecological difference equations accounting for feedbacks . Specifically, we use a stochastic analog of average Lyapunov functions to develop sufficient and necessary conditions for (i)
Edit intent: fluency
Original:  all population densities spending little time at low densities i.e. stochastic persistence , and (ii) population trajectories asymptotically approaching the extinction set with positive probability.
Revised:  all population densities spending little time at low densities , and (ii) population trajectories asymptotically approaching the extinction set with positive probability.
Edit intent: clarity
Original:  Furthermore, in the case of persistence, we provide lower bounds for the  time to escape neighborhoods of the extinction set.
Revised:  Furthermore, we provide lower bounds for the time to escape neighborhoods of the extinction set.
Edit intent: clarity
Original:  Furthermore, in the case of persistence, we provide lower bounds for the  time to escape neighborhoods of the extinction set.
Revised:  Furthermore, in the case of persistence, we provide lower bounds for the expected time to escape neighborhoods of the extinction set.
Edit intent: clarity
Original:  To illustrate the applicability of our results, we analyze  models of evolutionary games, stochastic Lotka-Volterra difference equations , trait evolution, and spatially structured disease dynamics.
Revised:  To illustrate the applicability of our results, we analyze stochastic models of evolutionary games, stochastic Lotka-Volterra difference equations , trait evolution, and spatially structured disease dynamics.
Edit intent: fluency
Original:  To illustrate the applicability of our results, we analyze  models of evolutionary games, stochastic Lotka-Volterra difference equations , trait evolution, and spatially structured disease dynamics.
Revised:  To illustrate the applicability of our results, we analyze models of evolutionary games, Lotka-Volterra difference equations , trait evolution, and spatially structured disease dynamics.
Edit intent: clarity
Original:  To illustrate the applicability of our results, we analyze  models of evolutionary games, stochastic Lotka-Volterra difference equations , trait evolution, and spatially structured disease dynamics.
Revised:  To illustrate the applicability of our results, we analyze models of evolutionary games, stochastic Lotka-Volterra dynamics , trait evolution, and spatially structured disease dynamics.
Edit intent: clarity
Original:  Our analysis of these models demonstrates environmental stochasticity facilitates coexistence  in the hawk-dove game, but inhibits coexistence in the rock-paper-scissors game and  Lotka-Volterra predator-prey model.
Revised:  Our analysis of these models demonstrates environmental stochasticity facilitates coexistence in the hawk-dove game, but inhibits coexistence in the rock-paper-scissors game and a Lotka-Volterra predator-prey model.
Edit intent: fluency
Original:  Furthermore, environmental fluctuations with positive auto-correlations can promote persistence of evolving populations and disease persistence in patchy landscapes.
Revised:  Furthermore, environmental fluctuations with positive auto-correlations can promote persistence of evolving populations and persistence of diseases in patchy landscapes.
Edit intent: clarity
Original:  While these results help close the gap between  persistence theories for deterministic and stochastic systems, we conclude by highlighting several challenges for future research.
Revised:  While our results help close the gap between persistence theories for deterministic and stochastic systems, we conclude by highlighting several challenges for future research.
Edit intent: clarity
Original:  While these results help close the gap between  persistence theories for deterministic and stochastic systems, we conclude by highlighting several challenges for future research.
Revised:  While these results help close the gap between the persistence theories for deterministic and stochastic systems, we conclude by highlighting several challenges for future research.
Edit intent: fluency
Original:  While these results help close the gap between  persistence theories for deterministic and stochastic systems, we conclude by highlighting several challenges for future research.
Revised:  While these results help close the gap between persistence theories for deterministic and stochastic systems, we highlight challenges for future research.
Edit intent: clarity
Original:  Autonomous robots increasingly depend on third-party off-the-shelf components and complex machine-learning techniques.
Revised: The recent drive towards achieving greater autonomy and intelligence in robotics has led to high levels of complexity. Autonomous robots increasingly depend on third-party off-the-shelf components and complex machine-learning techniques.
Edit intent: clarity
Original:  Autonomous robots increasingly depend on third-party off-the-shelf components and complex machine-learning techniques.
Revised:  Autonomous robots increasingly depend on third party off-the-shelf components and complex machine-learning techniques.
Edit intent: fluency
Original:  To address this challenge , we present SOTER, a programming framework that integrates the core principles of runtime assurance to enable the use of uncertified controllers , while still providing safety guarantees.
Revised:  To address these challenges , we present SOTER, a programming framework that integrates the core principles of runtime assurance to enable the use of uncertified controllers , while still providing safety guarantees.
Edit intent: fluency
Original:  To address this challenge , we present SOTER, a programming framework that integrates the core principles of runtime assurance to enable the use of uncertified controllers , while still providing safety guarantees.
Revised:  To address this challenge , we present SOTER, a programming framework that integrates the core principles of runtime assurance to enable the use of uncertified components , while still providing safety guarantees.
Edit intent: clarity
Original:  The compiler generates code for monitoring system state and switching control between the advanced and safecontroller in order to guarantee S. RTA allows complex systems to be constructed through the composition of RTA modules  .
Revised:  The compiler generates code for monitoring system state and switching control between the advanced and safecontroller in order to guarantee S. RTA allows complex systems to be constructed as a composition of RTA modules .
Edit intent: fluency
Original:  All the ideas presented in this paper have been implemented in a contract-based runtime verification system named EDBC .
Revised:  All the ideas presented in this paper have been implemented in a contract-based runtime verification system named EDBC .
Edit intent: fluency
Original: The paper is concerned with guaranteed and fully computable a posteriori error estimates for evolutionary problems associated with the poroelastic media governed by the quasi-static linear Biot equations (Biot, 1955).
Revised: The paper is concerned with guaranteed a posteriori error estimates for evolutionary problems associated with the poroelastic media governed by the quasi-static linear Biot equations (Biot, 1955).
Edit intent: clarity
Original: The paper is concerned with guaranteed and fully computable a posteriori error estimates for evolutionary problems associated with the poroelastic media governed by the quasi-static linear Biot equations (Biot, 1955).
Revised: The paper is concerned with guaranteed and fully computable a posteriori error estimates for a class of evolutionary problems related to poroelastic media governed by the quasi-static linear Biot equations (Biot, 1955).
Edit intent: clarity
Original:  The error bounds are applicable for any approximation from the admissible functional space and  independent of the discretisation methodused .
Revised:  The error bounds are applicable for any approximation in the admissible functional space and independent of the discretisation methodused .
Edit intent: clarity
Original:  The error bounds are applicable for any approximation from the admissible functional space and  independent of the discretisation methodused .
Revised:  The error bounds are applicable for any approximation from the admissible functional space and are independent of the discretisation methodused .
Edit intent: fluency
Original:  The error bounds are applicable for any approximation from the admissible functional space and  independent of the discretisation methodused .
Revised:  The error bounds are applicable for any approximation from the admissible functional space and independent of the discretization method .
Edit intent: coherence
Original:  They are fully computable and do not contain mesh dependent constants .
Revised:  They are fully computable , do not contain mesh dependent constants .
Edit intent: fluency
Original:  Functional estimates provide the reliable global estimates of the error measured in the terms of the energy normand suggest efficient error indicators for the distribution of local errors that is advantageous for automated mesh adaptation algorithms .
Revised:  Functional estimates provide the reliable global estimates of the error measured in the energy norm. Moreover, they suggest efficient error indicators for the distribution of local errors that is advantageous for automated mesh adaptation algorithms .
Edit intent: coherence
Original:  Functional estimates provide the reliable global estimates of the error measured in the terms of the energy normand suggest efficient error indicators for the distribution of local errors that is advantageous for automated mesh adaptation algorithms .
Revised:  Functional estimates provide the reliable global estimates of the error measured in the terms of the energy normand suggest efficient error indicators for the distribution of local errors , which can be used in adaptive procedures .
Edit intent: clarity
Original:  The more general property of confluence modulo equivalence ensures that equivalent inputs are related to equivalent outputs  that need not be identical  . Constraint Handling Rules (CHR) is an important example of a rewrite based logic programming language, and we aim at a mechanizable method for proving confluence modulo equivalence of terminating programs.
Revised:  The more general property of confluence modulo equivalence ensures that equivalent inputs are related to equivalent outputs , that need not be identical . Constraint Handling Rules (CHR) is an important example of a rewrite based logic programming language, and we aim at a mechanizable method for proving confluence modulo equivalence of terminating programs.
Edit intent: fluency
Original:  A central limit theorem is obtained also for the final size of the epidemic.
Revised:  A central limit theorem is conjectured for the final size of the epidemic.
Edit intent: clarity
Original:  The two versions yield the same limiting deterministic model but the asymptotic variances in the central limit theorems are greater in the Newman-Strogatz-Watts version.
Revised:  The two versions yield the same limiting deterministic model but the asymptotic variances in the central limit theorema are greater in the Newman-Strogatz-Watts version.
Edit intent: fluency
Original:  The basic reproduction number R_0 and the process of susceptible individuals in the limiting deterministic model  for the model with dropping of edges  are the same as for a corresponding SIR model without dropping of edges but an increased recovery rate, though, when R_0>1, the probability of a major outbreak is greater in the model with dropping of edges.
Revised:  The basic reproduction number R_0 and the process of susceptible individuals in the limiting deterministic model , for the model with dropping of edges are the same as for a corresponding SIR model without dropping of edges but an increased recovery rate, though, when R_0>1, the probability of a major outbreak is greater in the model with dropping of edges.
Edit intent: fluency
Original:  The basic reproduction number R_0 and the process of susceptible individuals in the limiting deterministic model  for the model with dropping of edges  are the same as for a corresponding SIR model without dropping of edges but an increased recovery rate, though, when R_0>1, the probability of a major outbreak is greater in the model with dropping of edges.
Revised:  The basic reproduction number R_0 and the process of susceptible individuals in the limiting deterministic model for the model with dropping of edges , are the same as for a corresponding SIR model without dropping of edges but an increased recovery rate, though, when R_0>1, the probability of a major outbreak is greater in the model with dropping of edges.
Edit intent: fluency
Original:  The results are specialised to the model without dropping of edges to yield in particular central limit theorems for the final size of Markovian SIR epidemics on configuration-model networks, and for the giant components of those networks.
Revised:  The results are specialised to the model without dropping of edges to yield conjectured central limit theorems for the final size of Markovian SIR epidemics on configuration-model networks, and for the giant components of those networks.
Edit intent: clarity