wanyu/IteraTeR_full_sent huggingface dataset:
Original:  We reinterpret the corresponding partitions of the state space into the continuation and stopping regions as statistical classification problems with noisy observations. Accordingly, a key new objective that we pursue is efficient design of the stochastic grids formed by the simulated sample paths of the underlying state process.
Revised:  Namely, we introduce adaptive generation of the stochastic grids formed by the simulated sample paths of the underlying state process.
Edit intent: clarity
Original:  We explore the combinatorics of reaction networks , with a view towards the Global Attractor Conjecture.
Revised: The persistence conjecture is a long-standing open problem in chemical reaction network theory. It concerns the behavior of solutions to coupled ODE systems that arise from applying mass-action kinetics to a network of chemical reactions. The idea is that if all reactions are reversible in a weak sense, then no species can go extinct. A notion that has been found useful in thinking about persistence is that of "critical siphon." We explore the combinatorics of reaction networks , with a view towards the Global Attractor Conjecture.
Edit intent: meaning-changed
Original:  We explore the combinatorics of reaction networks , with a view towards the Global Attractor Conjecture. We prove that full-rank matrices with positive off-diagonal and negative diagonal entries permit a positive linear combination of the rows so that all coordinates have the same sign. Using this, we show that a reaction network has critical siphons iff it has "drainable" or "self-replicable" siphons.
Revised:  We explore the combinatorics of reaction networks , with a view towards the persistence conjecture. We introduce the notions of "drainable" or "self-replicable" siphons.
Edit intent: clarity
Original:  Using this, we show that a reaction network has critical siphons iff it has "drainable" or "self-replicable" siphons. Further, if the minimal siphons of a reaction network are not drainable , then the dynamics is persistent. Consequently, we obtain a new, elementary proof for the persistence of non-catalytic weakly-reversible chemical reaction networks .
Revised:  Using this, we show that a reaction network has critical siphons iff it has "drainable" or "self-replicable" (or autocatalytic) siphons. We show that: every minimal critical siphon is either drainable or self-replicable; reaction networks without drainable siphons are persistent; and non-autocatalytic weakly-reversible chemical reaction networks .
Edit intent: clarity
Original: We consider networks with a specific type of nodes that can have either a discrete or continuous set of states. It is shown that no matter how complex the network is, its dynamical response to arbitrary inputs is defined in a simple way by its response to a monotone input.
Revised: We show that for a certain class of dynamics at the nodes the response of a network of any topology to arbitrary inputs is defined in a simple way by its response to a monotone input.
Edit intent: clarity
Original:   As illustrative applications, we propose and discuss a quasistatic mechanical model with objects interacting via friction forces, and a financial market model with avalanches and critical behavior induced by momentum trading strategies.
Revised:  The nodes may have either a discrete or continuous set of states and there is no limit on the complexity of the network. The results provide both an efficient numerical method and the potential for accurate analytic approximation of the dynamics on such networks. As illustrative applications, we propose and discuss a quasistatic mechanical model with objects interacting via friction forces, and a financial market model with avalanches and critical behavior induced by momentum trading strategies.
Edit intent: meaning-changed
Original:  We then show that the problem may readily be transformed into a Traveling Salesman Problem (TSP), so that the machinery that has been developed for the TSP may be applied to find optimal routes for the scaffolding strand in a DNA origami self-assembly process.
Revised:  We then show that the problem may readily be transformed into a Traveling Salesman Problem (TSP), so that machinery that has been developed for the TSP may be applied to find optimal routes for the scaffolding strand in a DNA origami self-assembly process.
Edit intent: fluency
Original:  The model predicts, under fairly general assumptions, the emergence of an hourglass pattern in terms of the number of state-transitioning genes during development. Additionally, the evolutionary age of those genes also follows an hourglass pattern, with the oldest genes concentrated at the hourglass waist.
Revised:  The model predicts, under fairly general assumptions, the emergence of an hourglass pattern in the structure of a temporal representation of the underlying gene regulatory network. The evolutionary age of those genes also follows an hourglass pattern, with the oldest genes concentrated at the hourglass waist.
Edit intent: clarity
Original:  Metabolic networks are often studied with optimization methods applied to constraint-based steady state models. But, a corresponding dynamic modeling framework including a tight interplay between metabolic fluxes and gene expression is currently lacking. Due to that, the cost of producing enzymes so far could not be taken into account in dynamic optimization of metabolic fluxes. Here , we present a modeling framework combining the metabolic network and the enzyme production costs.
Revised:  Metabolic networks are often studied at steady state using constraint-based models and optimization techniques. However, metabolic adaptations driven by changes in gene expression cannot be analyzed by steady state models, as these do not account for temporal changes in biomass composition. Here we present a modeling framework combining the metabolic network and the enzyme production costs.
Edit intent: clarity
Original:  Here , we present a modeling framework combining the metabolic network and the enzyme production costs. A rigorous mathematical approximation by a timescale separation yields a coupled model of quasi steady state constraints on the metabolic reactions, and differential equations for the substrate concentrations and biomass composition. Based on this model, we propose a dynamic optimization approach to determine reaction fluxes, explicitly taking production costs for enzymes and enzymatic capacity into account .
Revised:  Here , we present a modeling framework combining the metabolic network with the dynamics of biomass production and composition, explicitly taking into account enzyme production costs and enzymatic capacity into account .
Edit intent: clarity
Original:  In contrast to the established dynamic flux balance analysis, the proposed approach thereby allows to analyse dynamic changes in both the metabolic fluxes and the detailed biomass composition in situations of metabolic adaptation .
Revised:  In contrast to the established dynamic flux balance analysis, the proposed approach thereby allows to analyse dynamic changes in both the metabolic fluxes and the biomass composition during metabolic adaptations. We applied our algorithm in two case studies: a minimal nutrient uptake network, and an abstraction of core metabolic processes in bacteria. In the minimal model, we show that the optimized uptake rates reproduce the empirical Monod growth for bacterial cultures. For the network of core metabolic processes, the dynamic optimization algorithm predicted commonly observed metabolic adaptations, such as a diauxic switch with a preference ranking for different nutrients, re-utilization of waste products after depletion of the original substrate, and metabolic adaptation to an impending nutrient depletion. These examples illustrate how dynamic adaptations of enzyme expression can be predicted solely from an optimization principle .
Edit intent: meaning-changed
Original:  Here, we use 2H magnetic relaxation dispersion to selectively monitor water mobility in the core of Bacillus subtilis spores in the presence and absence of core Mn2+ ions.
Revised:  Here, we use 2H magnetic relaxation dispersion to selectively monitor water mobility in the core of Bacillus subtilis spores in the presence and absence of core Mn^{2+ ions.
Edit intent: fluency
Original:  For that, we perform an exhaustive computational screening of synthetic lethal reaction pairs in Escherichia coli in minimal medium and find that synthetic lethals divide in two different groups depending on whether the synthetic lethal interaction works as a back up or as a parallel use  , the first corresponding to essential plasticity and the second to essential redundancy.
Revised:  For that, we perform an exhaustive computational screening of synthetic lethal reaction pairs in Escherichia coli in minimal medium and find that synthetic lethals divide in two different groups depending on whether the synthetic lethal interaction works as a back up or as a parallel use mechanism , the first corresponding to essential plasticity and the second to essential redundancy.
Edit intent: clarity
Original:  In E. coli, the analysis of how pathways are entangled through essential plasticity and redundancy supports the view that synthetic lethality affects preferentially a single function or pathway , although with a major exception which unveils Cell Envelope Biosysthesis as an essential backup to Membrane Lipid Metabolism.
Revised:  In E. coli, the analysis of how pathways are entangled through essential redundancy supports the view that synthetic lethality affects preferentially a single function or pathway , although with a major exception which unveils Cell Envelope Biosysthesis as an essential backup to Membrane Lipid Metabolism.
Edit intent: clarity
Original:  In E. coli, the analysis of how pathways are entangled through essential plasticity and redundancy supports the view that synthetic lethality affects preferentially a single function or pathway , although with a major exception which unveils Cell Envelope Biosysthesis as an essential backup to Membrane Lipid Metabolism.
Revised:  In E. coli, the analysis of how pathways are entangled through essential plasticity and redundancy supports the view that synthetic lethality affects preferentially a single function or pathway . In contrast, essential plasticity, the dominant class, tends to be inter-pathway but concentrated and unveils Cell Envelope Biosysthesis as an essential backup to Membrane Lipid Metabolism.
Edit intent: meaning-changed
Original:  In E. coli, the analysis of how pathways are entangled through essential plasticity and redundancy supports the view that synthetic lethality affects preferentially a single function or pathway , although with a major exception which unveils Cell Envelope Biosysthesis as an essential backup to Membrane Lipid Metabolism.
Revised:  In E. coli, the analysis of how pathways are entangled through essential plasticity and redundancy supports the view that synthetic lethality affects preferentially a single function or pathway , although with a major exception which unveils Cell Envelope Biosynthesis as an essential backup to Membrane Lipid Metabolism.
Edit intent: fluency
Original:  We find that synthetic lethal interactions and their classification in plasticity and redundancy are basically insensitive to minimal medium composition, and are highly conserved even when the environment is enriched with nonessential compounds  .
Revised:  We find that synthetic lethal interactions and their classification in plasticity and redundancy are basically insensitive to minimal medium composition, and are highly conserved even when the environment is enriched with nonessential compounds or overconstrained to decrease maximum biomass formation .
Edit intent: meaning-changed
Original:  Investigating growth dynamics of a bundle of N independent cytoskeletal filaments pushing against a wall, we show that  ATP/GTP hydrolysis  leads to a collective phenomena that is currently unknown.
Revised:  Investigating growth dynamics of a bundle of N independent cytoskeletal filaments pushing against a wall, we show that chemical switching ( ATP/GTP hydrolysis leads to a collective phenomena that is currently unknown.
Edit intent: meaning-changed
Original:  Simulating growing actin and microtubule bundles, considering both sequential and random hydrolysis, we make quantitative predictions of the excess forces  .
Revised:  Employing an exactly solvable toy model, we analytically prove the above result for N=2. We, further, numerically show the existence of this collective phenomenon, for N>=2, in realistic models (with random and sequential hydrolysis) that simulate actin and microtubule bundle growth. We make quantitative predictions of the excess forces .
Edit intent: meaning-changed
Original:  Simulating growing actin and microtubule bundles, considering both sequential and random hydrolysis, we make quantitative predictions of the excess forces  .
Revised:  Simulating growing actin and microtubule bundles, considering both sequential and random hydrolysis, we make quantitative predictions of the excess forces , and argue that this collective effect is related to the non-equilibrium nature of chemical switching .
Edit intent: meaning-changed
Original:  For example, while past intraday returns affect equally the future intraday and overnight volatilities, past overnight returns have a weak effect on future intraday volatilities (except for the very next one) but impact substantially future overnight volatilities.
Revised:  For example, while past intra-day returns affect equally the future intraday and overnight volatilities, past overnight returns have a weak effect on future intraday volatilities (except for the very next one) but impact substantially future overnight volatilities.
Edit intent: clarity
Original:  For example, while past intraday returns affect equally the future intraday and overnight volatilities, past overnight returns have a weak effect on future intraday volatilities (except for the very next one) but impact substantially future overnight volatilities.
Revised:  For example, while past intraday returns affect equally the future intra-day and overnight volatilities, past overnight returns have a weak effect on future intraday volatilities (except for the very next one) but impact substantially future overnight volatilities.
Edit intent: clarity
Original:  For example, while past intraday returns affect equally the future intraday and overnight volatilities, past overnight returns have a weak effect on future intraday volatilities (except for the very next one) but impact substantially future overnight volatilities.
Revised:  For example, while past intraday returns affect equally the future intraday and overnight volatilities, past overnight returns have a weak effect on future intra-day volatilities (except for the very next one) but impact substantially future overnight volatilities.
Edit intent: clarity
Original:  We provide a plausible interpretation for these findings, and show that our IntraDay /Overnight model significantly outperforms the standard ARCH framework based on daily returns for Out-of-Sample predictions.
Revised:  We provide a plausible interpretation for these findings, and show that our Intra-Day /Overnight model significantly outperforms the standard ARCH framework based on daily returns for Out-of-Sample predictions.
Edit intent: fluency
Original:  To identify patterns of molecular function and genetic diversity in GRNs, we studied the drought response of the common sunflower, Helianthus annuus, and how the underlying GRN has influenced its evolution.
Revised:  To identify patterns of molecular function and genetic diversity in GRNs, we studied the drought response of the common sunflower, Helianthus annuus, and how the underlying GRN is related to its evolution.
Edit intent: clarity
Original: This paper extends results from Mortimer and Williams (1991) about changes of probability measure up to random times. Many new classes of examples involving honest times and pseudo-stopping times are provided .
Revised: This paper extends results from Mortimer and Williams (1991) about changes of probability measure up to a random time under the assumptions that all martingales are continuous and that the random time avoids stopping times. We consider locally absolutely continuous measure changes up to a random time, changes of probability measure up to and after an honest time, and changes of probability measure up to a pseudo-stopping times are provided .
Edit intent: meaning-changed
Original:   In this paper, we propose an empirical study on the Korean and Hong Kong stock market with an integrated machine learning framework that employs Principal Component Analysis (PCA) and Support Vector Machine (SVM).
Revised:  Many stock prediction studies focus on using macroeconomic indicators, such as CPI and GDP, to train the prediction model. However, daily data of the macroeconomic indicators are almost impossible to obtain. Thus, those methods are difficult to be employed in practice. In this paper, we propose an empirical study on the Korean and Hong Kong stock market with an integrated machine learning framework that employs Principal Component Analysis (PCA) and Support Vector Machine (SVM).
Edit intent: meaning-changed
Original:  We try to predict the upward or downward direction of stock market index and stock price . In the proposed framework, PCA, as a feature selection method, identifies principal components in the stock market movement and SVM, as a classifier for future stock market movement, processes them along with other economic factors in training and forecasting. We present the results of an extensive empirical study of the proposed method  on the Korean composite stock price index (KOSPI) and Hangseng index (HSI), as well as the individual constituents included in the indices.
Revised:  We try to predict the upward or downward direction of stock market index and stock price direction. An extensive empirical study of the proposed method on the Korean composite stock price index (KOSPI) and Hangseng index (HSI), as well as the individual constituents included in the indices.
Edit intent: clarity
Original:  We present the results of an extensive empirical study of the proposed method  on the Korean composite stock price index (KOSPI) and Hangseng index (HSI), as well as the individual constituents included in the indices.
Revised:  We present the results of an extensive empirical study of the proposed method is presented on the Korean composite stock price index (KOSPI) and Hangseng index (HSI), as well as the individual constituents included in the indices.
Edit intent: meaning-changed
Original:  We present the results of an extensive empirical study of the proposed method  on the Korean composite stock price index (KOSPI) and Hangseng index (HSI), as well as the individual constituents included in the indices.
Revised:  We present the results of an extensive empirical study of the proposed method on the Korean Composite Stock Price Index (KOSPI) and Hangseng index (HSI), as well as the individual constituents included in the indices.
Edit intent: fluency
Original:  We present the results of an extensive empirical study of the proposed method  on the Korean composite stock price index (KOSPI) and Hangseng index (HSI), as well as the individual constituents included in the indices.
Revised:  We present the results of an extensive empirical study of the proposed method on the Korean composite stock price index (KOSPI) and Hang Seng Index (HSI), as well as the individual constituents included in the indices.
Edit intent: fluency
Original:  The experimental results show notably high hit ratios in predicting the movements of the individual constituents in the KOSPI and HSI. The results also varify theco-movement effect between the Korean (Hong Kong) stock market and the American stock market .
Revised:  The experimental results show notably high hit ratios in predicting the movements of the individual constituents in the KOSPI and co-movement effect between the Korean (Hong Kong) stock market and the American stock market .
Edit intent: clarity
Original:  Our pipeline for viewing angle classification and alignment is experimentally shown to be faster and more accurate than reference-free alignment with rotationally invariant K-means clustering and MSA/MRA 2D classification  .
Revised:  Our pipeline for viewing angle classification and alignment is experimentally shown to be faster and more accurate than reference-free alignment with rotationally invariant K-means clustering , MSA/MRA 2D classification .
Edit intent: coherence
Original:  Our pipeline for viewing angle classification and alignment is experimentally shown to be faster and more accurate than reference-free alignment with rotationally invariant K-means clustering and MSA/MRA 2D classification  .
Revised:  Our pipeline for viewing angle classification and alignment is experimentally shown to be faster and more accurate than reference-free alignment with rotationally invariant K-means clustering and MSA/MRA 2D classification , and their modern approximations .
Edit intent: meaning-changed
Original:  We show that the behaviour at small strikes is uniquely determined by the mass of the atom at least up to the third asymptotic order, regardless of the properties of the remaining (absolutely continuous, or singular) distribution on the positive real line.
Revised:  We show that the behaviour at small strikes is uniquely determined by the mass of the atom up to the third asymptotic order, regardless of the properties of the remaining (absolutely continuous, or singular) distribution on the positive real line.
Edit intent: clarity
Original:  We show that the behaviour at small strikes is uniquely determined by the mass of the atom at least up to the third asymptotic order, regardless of the properties of the remaining (absolutely continuous, or singular) distribution on the positive real line.
Revised:  We show that the behaviour at small strikes is uniquely determined by the mass of the atom at least up to the third asymptotic order, under mild assumptions on the remaining distribution on the positive real line.
Edit intent: clarity
Original:  Note that while Lee's moment formula tells that implied variance is at most asymptotically linear in log-strike, other celebrated results for exact smile asymptotics such as Benaim and Friz (09) or Gulisashvili (10) do not apply in this setting-essentially due to the breakdown of Put-Call symmetry-and we rely here on an alternative treatment of the problem.
Revised:  Note that while Lee's moment formula tells that implied variance is at most asymptotically linear in log-strike, other celebrated results for exact smile asymptotics such as Benaim and Friz (09) or Gulisashvili (10) do not apply in this setting--essentially due to the breakdown of Put-Call symmetry-and we rely here on an alternative treatment of the problem.
Edit intent: fluency
Original:  Note that while Lee's moment formula tells that implied variance is at most asymptotically linear in log-strike, other celebrated results for exact smile asymptotics such as Benaim and Friz (09) or Gulisashvili (10) do not apply in this setting-essentially due to the breakdown of Put-Call symmetry-and we rely here on an alternative treatment of the problem.
Revised:  Note that while Lee's moment formula tells that implied variance is at most asymptotically linear in log-strike, other celebrated results for exact smile asymptotics such as Benaim and Friz (09) or Gulisashvili (10) do not apply in this setting-essentially due to the breakdown of Put-Call symmetry--and one has to rely on a new treatment of the problem.
Edit intent: clarity