wanyu/IteraTeR_full_sent huggingface dataset:
Original:   . Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in ribosomes bound to multiple mRNAs . Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.
Revised:  and budding yeast . Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in ribosomes bound to multiple mRNAs . Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.
Edit intent: clarity
Original:   . Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in ribosomes bound to multiple mRNAs . Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.
Revised:  . Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in polysomes . Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.
Edit intent: clarity
Original: We present a set of analyses aiming at quantifying the amount of information filtered by different hierarchical clustering methods on correlations between stock returns . In particular we apply, for the first time to financial data, a novel hierarchical clustering approach, the Directed Bubble Hierarchical Tree (DBHT), and we compare it with other methods including the Linkage and k-medoids.
Revised: We present a set of analyses aiming at quantifying the amount of information filtered by different hierarchical clustering methods on correlations between stock returns comparing it with the underlying industrial activity structure. Specifically, we apply, for the first time to financial data, a novel hierarchical clustering approach, the Directed Bubble Hierarchical Tree (DBHT), and we compare it with other methods including the Linkage and k-medoids.
Edit intent: meaning-changed
Original:  In particular we apply, for the first time to financial data, a novel hierarchical clustering approach, the Directed Bubble Hierarchical Tree (DBHT), and we compare it with other methods including the Linkage and k-medoids.
Revised:  In particular we apply, for the first time to financial data, a novel hierarchical clustering approach, the Directed Bubble Hierarchical Tree and we compare it with other methods including the Linkage and k-medoids.
Edit intent: clarity
Original:  The computational cost of the deterministic approximation is significantly lower  but the diffusion approximation retains stochasticity and is able to reproduce relevant random features like variance, bimodality, and tail behavior that cannot be captured by a single deterministic quantity .
Revised:  The computational cost of the deterministic approximation is significantly lower , but the diffusion approximation retains stochasticity and is able to reproduce relevant random features like variance, bimodality, and tail behavior that cannot be captured by a single deterministic quantity .
Edit intent: fluency
Original:  The computational cost of the deterministic approximation is significantly lower  but the diffusion approximation retains stochasticity and is able to reproduce relevant random features like variance, bimodality, and tail behavior that cannot be captured by a single deterministic quantity .
Revised:  The computational cost of the deterministic approximation is significantly lower but the diffusion approximation retains stochasticity and is able to reproduce relevant random features like variance, bimodality, and tail behavior .
Edit intent: clarity
Original:  In a recent paper, for particular stochastic Petri net models, we proposed a jump diffusion approximation that extends Kurtz's diffusion approximation to the case when the process reaches the boundary with non-negligible probability.
Revised:  In a recent paper, for particular stochastic Petri net models, we proposed a jump diffusion approximation that aims at being applicable beyond the limits of Kurtz's diffusion approximation to the case when the process reaches the boundary with non-negligible probability.
Edit intent: meaning-changed
Original:  In a recent paper, for particular stochastic Petri net models, we proposed a jump diffusion approximation that extends Kurtz's diffusion approximation to the case when the process reaches the boundary with non-negligible probability.
Revised:  In a recent paper, for particular stochastic Petri net models, we proposed a jump diffusion approximation that extends Kurtz's diffusion approximation , namely when the process reaches the boundary with non-negligible probability.
Edit intent: clarity
Original:  Other limitations of the diffusion approximation  are that it can provide inaccurate results when the number of objects in some groups is often or constantly low and that it can be applied only to pure density dependent Markov chains.
Revised:  Other limitations of the diffusion approximation in its original form are that it can provide inaccurate results when the number of objects in some groups is often or constantly low and that it can be applied only to pure density dependent Markov chains.
Edit intent: meaning-changed
Original:  We show that the stochastic differential equations that characterize this process can be derived automatically both from the description of the original Markov chain or starting from the correspondent Petri net .
Revised:  We show that the stochastic differential equations that characterize this process can be derived automatically both from the description of the original Markov chain or starting from a higher level description language, like stochastic Petri nets .
Edit intent: meaning-changed
Original:  This paper proposes a generalized multi-currency pricing and hedging framework that allows the flexibility of choosing the perspective from which funding is managed for each currency . When cross currency basis spreads collapse to zero , this method  converges to the well established single currency setting in which each leg is funded in its own currency.
Revised:  This paper proposes a generalized multi-currency pricing and hedging which allows taking into account the funding and therefore the collateral currency and its pricing impact. For uncollateralized operations, it provides more funding optionality to achieve either cheaper or more connected funding to the hedging instruments. When foreign exchange forwards get aligned with overnight cash and carry arguments , this method converges to the well established single currency setting in which each leg is funded in its own currency.
Edit intent: meaning-changed
Original:  Focusing on FX data (EBS limit order book) with 0.1s time resolution, we find that significance is impossible if the event log is incomplete (e. g. best quote changes). Transactions on the other hand can be tracked by analysing the respective volumes of transactions on both sides in each time slice. Assuming a constant exogenous activity rate and using parametric kernels , fits of trade activity satisfy Kolmogorov-Smirnov tests for about an hour , provided that the kernel consists of at least two exponentials; the endogeneity factor does not depend on the time of the day and is about 0.7. Significant fits of a full day can be achieved if one accounts for intra-day variability of exogenous activity, which yields a larger endogeneity factor ( 0.8 ).
Revised:  This raises the question of what part of market dynamics this model is able to account for exactly. We document the accuracy of such processes as one varies the time interval of calibration and compare the performance of various types of kernels made up of sums of exponentials. Because of their around-the-clock opening times, FX markets are ideally suited to our aim as they allow us to avoid the complications of the long daily overnight closures of equity markets. One can achieve statistical significance according to three simultaneous tests provided that one uses kernels with two exponentials for fitting an hour at a time, and two or three exponentials for full days, while longer periods could not be fitted within statistical satisfaction because of the non-stationarity of the endogenous process. Fitted timescales are relatively short and endogeneity factor is high but sub-critical at about 0.8 ).
Edit intent: clarity
Original:  the endogeneity factor does not depend on the time of the day and is about 0.7. Significant fits of a full day can be achieved if one accounts for intra-day variability of exogenous activity, which yields a larger endogeneity factor ( 0.8 ). We could not obtain significant fits beyond a single day. Variable seasonalities are major obstacles to fitting FX activity with Hawkes processes accurately and result in larger apparent endogeneity factors and lower statistical significance .
Revised:  the endogeneity factor does not depend on the time of the day and is about 0.7. Significant fits of a full day can be achieved if one accounts for intra-day variability of exogenous activity, which yields a larger endogeneity factor ( 0.8 .
Edit intent: coherence
Original:  In a general semimartingale setting, we provide an HJM approach to model the term structure of multiplicative spreads between (normalized) FRA rates and simply compounded OIS risk-free forward rates.
Revised:  In a general semimartingale setting, we provide an HJM approach to model the term structure of multiplicative spreads between FRA rates and simply compounded OIS risk-free forward rates.
Edit intent: clarity
Original: We show that a mesoscale model, with a minimal number of parameters, can describe well the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque.
Revised: We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque.
Edit intent: fluency
Original:  We find strong agreement with available single molecule manipulation experiments  .
Revised:  We find strong agreement with available single molecule manipulation experiments and find strong agreement. In particular we elucidate the difference between angularly constrained and unconstrained overstretching. We propose that the smoothness of the angularly constrained overstreching transition is a consequence of the molecule being in the vicinity of criticality for a broad range of values of applied tension .
Edit intent: meaning-changed
Original:  Using a recent theory of singular changes of measures for Ito processes, we formulate a principal-agent problem in this context, and solve it in the case of CARA preferences .
Revised:  We identify a family of admissible contracts for which the optimal agent's action is explicitly characterized, and, using the recent theory of singular changes of measures for Ito processes, we formulate a principal-agent problem in this context, and solve it in the case of CARA preferences .
Edit intent: meaning-changed
Original:  Using a recent theory of singular changes of measures for Ito processes, we formulate a principal-agent problem in this context, and solve it in the case of CARA preferences .
Revised:  Using a recent theory of singular changes of measures for Ito processes, we study how restrictive this family is. In particular, in the special case of the standard Homlstr\"om-Milgrom model with fixed volatility, the family includes all possible contracts. We solve the principal-agent problem in this context, and solve it in the case of CARA preferences .
Edit intent: meaning-changed
Original:  Using a recent theory of singular changes of measures for Ito processes, we formulate a principal-agent problem in this context, and solve it in the case of CARA preferences . In that case, the optimal contract is linear in these factors: the contractible sources of risk, including the output, the quadratic variation of the output and the cross-variations between the output and the contractible risk sources.
Revised:  Using a recent theory of singular changes of measures for Ito processes, we formulate a principal-agent problem in this context, and solve it in the case of CARA preferences , and show that the optimal contract is linear in these factors: the contractible sources of risk, including the output, the quadratic variation of the output and the cross-variations between the output and the contractible risk sources.
Edit intent: coherence
Original:  We have implemented the algorithm in MATLAB, building upon COBRA toolbox v2.0 . Fast-SL also compares favourably with SL Finder, an algorithm for identifying synthetic lethal sets, by Suthers et al (2009), which involves the solution of  bi-level Mixed Integer Linear Programming problem  .
Revised:  Fast-SL offers a substantial speed-up through a massive reduction in the search space for synthetic lethals; in the case of E. coli, Fast-SL reduces the search space for synthetic lethal triplets by over 4000-fold . Fast-SL also compares favourably with SL Finder, an algorithm for identifying synthetic lethal sets, by Suthers et al (2009), which involves the solution of bi-level Mixed Integer Linear Programming problem .
Edit intent: meaning-changed
Original:  We have implemented the algorithm in MATLAB, building upon COBRA toolbox v2.0 . Fast-SL also compares favourably with SL Finder, an algorithm for identifying synthetic lethal sets, by Suthers et al (2009), which involves the solution of  bi-level Mixed Integer Linear Programming problem  .
Revised:  We have implemented the algorithm in MATLAB, building upon COBRA toolbox v2.0 . Fast-SL also compares favourably with SL Finder, an algorithm for identifying synthetic lethal sets, by Suthers et al (2009), which involves the solution of a bi-level Mixed Integer Linear Programming problem .
Edit intent: fluency
Original:  We have implemented the algorithm in MATLAB, building upon COBRA toolbox v2.0 . Fast-SL also compares favourably with SL Finder, an algorithm for identifying synthetic lethal sets, by Suthers et al (2009), which involves the solution of  bi-level Mixed Integer Linear Programming problem  .
Revised:  We have implemented the algorithm in MATLAB, building upon COBRA toolbox v2.0 . Fast-SL also compares favourably with SL Finder, an algorithm for identifying synthetic lethal sets, by Suthers et al (2009), which involves the solution of bi-level Mixed Integer Linear Programming problem . We have implemented the Fast-SL algorithm in MATLAB, building upon COBRA toolbox v2.0 .
Edit intent: clarity
Original:  However, due to respective technical idiosyncrasies , they might produce modular descriptions that provide networkpictures at different resolution levels. We aimed to analyze how these alternative modular descriptions could condition the outcome of follow-up network biology analysis.
Revised:  However, due to respective technical idiosyncrasies , they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how these alternative modular descriptions could condition the outcome of follow-up network biology analysis.
Edit intent: clarity
Original:  We analyzed at what extent both procedures yielded different results in terms of cluster sizes, their biological congruencyand displayed meso-scale connectivity patterns.
Revised:  We analyzed at what extent both procedures yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns.
Edit intent: meaning-changed
Original:  We specifically studied the case of aging related proteins, and showed that only the high-resolution modular description , achieved by infomap, could unveil statistically significant associations between them and inter/intra modular connectivity schemes.
Revised:  As a case study we considered a set of aging related proteins, and showed that only the high-resolution modular description , achieved by infomap, could unveil statistically significant associations between them and inter/intra modular connectivity schemes.
Edit intent: clarity
Original:  We specifically studied the case of aging related proteins, and showed that only the high-resolution modular description , achieved by infomap, could unveil statistically significant associations between them and inter/intra modular connectivity schemes.
Revised:  We specifically studied the case of aging related proteins, and showed that only the high-resolution modular description provided by infomap, could unveil statistically significant associations between them and inter/intra modular connectivity schemes.
Edit intent: clarity
Original:  We specifically studied the case of aging related proteins, and showed that only the high-resolution modular description , achieved by infomap, could unveil statistically significant associations between them and inter/intra modular connectivity schemes. In particular, we found that aging related proteins were more likely to reside in the interface of network modules, possibly linking distinct biological processes.
Revised:  We specifically studied the case of aging related proteins, and showed that only the high-resolution modular description , achieved by infomap, could unveil statistically significant associations between them and inter-intra modular cartographic features.
Edit intent: clarity
Original:  Besides reporting novel biological insights that could be gained from the discovered associations, our results warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies  .
Revised:  Besides reporting novel biological insights that could be gained from the discovered associations, our results warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies . In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge .
Edit intent: meaning-changed
Original:  However, there seems to be no satisfactory answer, in conventional economic theories and models, to the fundamental question of what kind of pay distribution we ought to see in a free market environment , at least under ideal conditions  .
Revised:  However, there seems to be no satisfactory answer, in conventional economic theories and models, to the fundamental question of what kind of pay distribution we ought to see in a free market environment , at least under ideal conditions , in a free market environment and whether this distribution is fair .
Edit intent: meaning-changed
Original:  We propose a novel game theoretic framework that addresses this question and shows that the lognormal distribution is the fairest inequality of pay in URLanization  , achieved at equilibrium, under ideal free market conditions  .
Revised:  We propose a novel game theoretic framework that addresses these questions and show that the lognormal distribution is the fairest inequality of pay in URLanization , achieved at equilibrium, under ideal free market conditions .
Edit intent: fluency
Original:  We propose a novel game theoretic framework that addresses this question and shows that the lognormal distribution is the fairest inequality of pay in URLanization  , achieved at equilibrium, under ideal free market conditions  .
Revised:  We propose a novel game theoretic framework that addresses this question and shows that the lognormal distribution is the fairest inequality of pay in URLanization comprising of homogenous agents , achieved at equilibrium, under ideal free market conditions .
Edit intent: meaning-changed
Original:  We propose a novel game theoretic framework that addresses this question and shows that the lognormal distribution is the fairest inequality of pay in URLanization  , achieved at equilibrium, under ideal free market conditions  .
Revised:  We propose a novel game theoretic framework that addresses this question and shows that the lognormal distribution is the fairest inequality of pay in URLanization , achieved at equilibrium, under ideal free market conditions . We also show that for a population of two different classes of agents, the final distribution is a combination of two different lognormal distributions where one of them, corresponding to the top 3-5\% of the population, can be misidentified as a Pareto distribution .
Edit intent: meaning-changed
Original:  Geometric Arbitrage Theory , where a generic market is modelled with a principal fibre bundle and arbitrage corresponds to its curvature, is applied to credit marketsto model default risk and recovery, leading to closed form no arbitrage characterizations for corporate bonds  .
Revised: We apply Geometric Arbitrage Theory , where a generic market is modelled with a principal fibre bundle and arbitrage corresponds to its curvature, is applied to credit marketsto model default risk and recovery, leading to closed form no arbitrage characterizations for corporate bonds .
Edit intent: fluency
Original:  Geometric Arbitrage Theory , where a generic market is modelled with a principal fibre bundle and arbitrage corresponds to its curvature, is applied to credit marketsto model default risk and recovery, leading to closed form no arbitrage characterizations for corporate bonds  .
Revised:  Geometric Arbitrage Theory to obtain results in mathematical finance for credit markets, which do not need stochastic differential geometry in their formulation. We obtain closed form equations involving default intensities and loss given defaults characterizing the no-free-lunch-with-vanishing-risk condition for corporate bonds .
Edit intent: meaning-changed
Original:  Geometric Arbitrage Theory , where a generic market is modelled with a principal fibre bundle and arbitrage corresponds to its curvature, is applied to credit marketsto model default risk and recovery, leading to closed form no arbitrage characterizations for corporate bonds  .
Revised:  Geometric Arbitrage Theory , where a generic market is modelled with a principal fibre bundle and arbitrage corresponds to its curvature, is applied to credit marketsto model default risk and recovery, leading to closed form no arbitrage characterizations for corporate bonds , as well as the generic dynamics for credit market allowing for arbitrage possibilities. Moreover, arbitrage credit bubbles for both base credit assets and credit derivatives are explicitly computed for the market dynamics minimizing the arbitrage .
Edit intent: meaning-changed