wanyu/IteraTeR_full_sent huggingface dataset:
Original:  On 15 crystallographic datasetsfor ribozymes, riboswitches, and other RNA domains, ERRASER/PHENIX corrects the majority of identifiable sugar pucker errors, steric clashes , suspicious backbone rotamers, and incorrect bond lengths/angles, while, on average, improving Rfree correlation to set-aside diffraction data by 0.010. As further confirmation of improved accuracy, the refinement enhances agreement between crystals solved by independent groups and between domains related by non-crystallographic symmetry (NCS). Finally, we demonstrate successful application of ERRASER on coordinates for an entire 30S ribosomal subunit. By rapidly and systematically disambiguating RNA model fitting, ERRASER enables RNA crystallography with significantly fewer errors .
Revised:  On 15 crystallographic datasetsfor ribozymes, riboswitches, and other RNA domains, ERRASER/PHENIX corrects the majority of steric clashes and anomalous backbone and bond geometries, as assessed by MolProbity. Furthermore, the method improves the average Rfree by 0.014, resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution structures to better match higher resolution structures. By enabling such 'super-resolution' interpretation of crystallographic data, ERRASER is a unique application of RNA structure prediction that promises routine use in experimental structural biology .
Edit intent: meaning-changed
Original: RNA crystallographic models contain pervasive ambiguities due to the difficulty of manually fitting RNA backbones into experimental density maps . Recent advances in ab initio RNA structure prediction suggest an automated way to resolve these ambiguities. We present a protocol for Enumerative Real-space Refinement ASsisted by Electron density under Rosetta (ERRASER), coupled to PHENIX diffraction-based refinement.
Revised: Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by electron density under Rosetta (ERRASER), coupled to PHENIX diffraction-based refinement.
Edit intent: meaning-changed
Original:  We present a protocol for Enumerative Real-space Refinement ASsisted by Electron density under Rosetta (ERRASER), coupled to PHENIX diffraction-based refinement.
Revised:  We present a protocol for Enumerative Real-space Refinement ASsisted by Electron density under Rosetta (ERRASER), coupled to Python-based hierarchical environment for integrated 'xtallography' (PHENIX) diffraction-based refinement.
Edit intent: meaning-changed
Original:  On 24 RNA crystallographic datasets, including a 30S ribosomal subunit and an unreleased IRES domain of hepatitis C virus, the protocol corrects the majority of steric clashes and anomalous backbone and bond geometries, as assessed by MolProbity.
Revised:  On 24 data sets, ERRASER automatically corrects the majority of steric clashes and anomalous backbone and bond geometries, as assessed by MolProbity.
Edit intent: clarity
Original:  On 24 RNA crystallographic datasets, including a 30S ribosomal subunit and an unreleased IRES domain of hepatitis C virus, the protocol corrects the majority of steric clashes and anomalous backbone and bond geometries, as assessed by MolProbity. Furthermore, the method improves the average Rfree by 0.014 , resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution structures to better match higher resolution structures.
Revised:  On 24 RNA crystallographic datasets, including a 30S ribosomal subunit and an unreleased IRES domain of hepatitis C virus, the protocol corrects the majority of MolProbity-assessed errors, improves the average Rfree by 0.014 , resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution structures to better match higher resolution structures.
Edit intent: clarity
Original:  Furthermore, the method improves the average Rfree by 0.014 , resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution structures to better match higher resolution structures.
Revised:  Furthermore, the method improves the average Rfree factor , resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution structures to better match higher resolution structures.
Edit intent: clarity
Original:  Furthermore, the method improves the average Rfree by 0.014 , resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution structures to better match higher resolution structures.
Revised:  Furthermore, the method improves the average Rfree by 0.014 , resolves functionally important discrepancies in noncanonical structure and refines low-resolution structures to better match higher resolution structures.
Edit intent: meaning-changed
Original:  Furthermore, the method improves the average Rfree by 0.014 , resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution structures to better match higher resolution structures.
Revised:  Furthermore, the method improves the average Rfree by 0.014 , resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution models to better match higher resolution structures.
Edit intent: clarity
Original:  Furthermore, the method improves the average Rfree by 0.014 , resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution structures to better match higher resolution structures. By enabling such 'super-resolution' interpretation of crystallographic data, ERRASER is a unique application of RNA structure prediction that promises routine use in experimental structural biology .
Revised:  Furthermore, the method improves the average Rfree by 0.014 , resolves functionally important discrepancies in protein-binding kink turns and group I ribozyme active sites, and refines low-resolution structures to better match higher-resolution models .
Edit intent: clarity
Original: We analyze pricing and portfolio optimization problems in defaultable regime switching markets. We contribute to both of these problems by obtaining novel characterizations of option prices and optimal portfolio strategies under regime-switching . Using our option price representation, we develop a novel efficient method to price claims which may depend on the full path of the underlying Markov chain.
Revised: Using a suitable change of probability measure, we obtain a novel Poisson series representation for the arbitrage- free price process of vulnerable contingent claims in a regime-switching . Using our option price representation, we develop a novel efficient method to price claims which may depend on the full path of the underlying Markov chain.
Edit intent: meaning-changed
Original:  We contribute to both of these problems by obtaining novel characterizations of option prices and optimal portfolio strategies under regime-switching . Using our option price representation, we develop a novel efficient method to price claims which may depend on the full path of the underlying Markov chain. This is done via a change of probability measure and a short-time asymptotic expansion of the claim's price in terms of the Laplace transforms of the symmetric Dirichlet distribution .
Revised:  We contribute to both of these problems by obtaining novel characterizations of option prices and optimal portfolio strategies under regime-switching market driven by an underlying continuous- time Markov process. As a result of this representation, along with a short-time asymptotic expansion of the claim's price in terms of the Laplace transforms of the symmetric Dirichlet distribution .
Edit intent: clarity
Original:  This is done via a change of probability measure and a short-time asymptotic expansion of the claim's price in terms of the Laplace transforms of the symmetric Dirichlet distribution .
Revised:  This is done via a change of probability measure and a short-time asymptotic expansion of the claim's price process, we develop an efficient method for pricing claims whose payoffs may depend on the full path of the underlying Markov chain .
Edit intent: meaning-changed
Original:  The proposed approach is applied to price not only simple European claims such as defaultable bonds, but also a new type of path-dependent claims that we term self-decomposable  as well as the important class of vulnerable call and put options on a stock.
Revised:  The proposed approach is applied to price not only simple European claims such as defaultable bonds, but also a new type of path-dependent claims that we term self-decomposable , as well as the important class of vulnerable call and put options on a stock.
Edit intent: fluency
Original:  In the portfolio optimization context, we obtain explicit constructions of value functions and investment strategies for investors with Constant Relative Risk Aversion (CRRA) utilities, built on the Hamilton-Jacobi-Bellman (HJB) framework developed in Capponi and Figueroa-Lopez (2011). We give a precise characterization of the investment strategies in terms of corporate bond returns, forward rates, and expected recovery at default, and illustrate the dependence of the optimal strategies on time, losses given default, and risk aversion level of the investor through a detailed economical analysis .
Revised:  We provide a detailed error analysis and illustrate the accuracy and computational complexity of our method on several market traded instruments, such as defaultable bond prices, barrier options, and vulnerable call options. Using again our Poisson series representation, we show differentiability in time of the pre-default price function of European vulnerable claims, which enables us to rigorously deduce Feynman-Kac representations for the pre-default pricing function and new semimartingale representations for the price process of the vulnerable claim under both risk-neutral and objective probability measures .
Edit intent: meaning-changed
Original: We present a novel methodology to determine the fundamental value of firms in the social-networking sector , motivated by recent realized IPOs and by reports that suggest sky-high valuations of firms such as facebook, Groupon, LinkedIn Corp., Pandora Media Inc, Twitter, Zynga. Our valuation of these firms is based on two ingredients: (i) revenues and profits of a social-networking firm are inherently linked to its user basis through a direct channel that has no equivalent in other sectors;
Revised: We present a novel methodology to determine the fundamental value of firms in the social-networking sector based on two ingredients: (i) revenues and profits of a social-networking firm are inherently linked to its user basis through a direct channel that has no equivalent in other sectors;
Edit intent: coherence
Original:  Illustrating the methodology with  facebook, one of the biggest of the social-media giants , we find a clear signature of a change of regime that occurred in 2010 on the growth of the number of users, from a pure exponential behavior (a paradigm for unlimited growth) to a logistic function describing the evolution towards an asymptotic plateau (a paradigm for growth in competition).
Revised:  We illustrate the methodology with facebook, one of the biggest of the social-media giants , we find a clear signature of a change of regime that occurred in 2010 on the growth of the number of users, from a pure exponential behavior (a paradigm for unlimited growth) to a logistic function describing the evolution towards an asymptotic plateau (a paradigm for growth in competition).
Edit intent: clarity
Original:  Illustrating the methodology with  facebook, one of the biggest of the social-media giants , we find a clear signature of a change of regime that occurred in 2010 on the growth of the number of users, from a pure exponential behavior (a paradigm for unlimited growth) to a logistic function describing the evolution towards an asymptotic plateau (a paradigm for growth in competition).
Revised:  Illustrating the methodology with a detailed analysis of facebook, one of the biggest of the social-media giants , we find a clear signature of a change of regime that occurred in 2010 on the growth of the number of users, from a pure exponential behavior (a paradigm for unlimited growth) to a logistic function describing the evolution towards an asymptotic plateau (a paradigm for growth in competition).
Edit intent: meaning-changed
Original:  Illustrating the methodology with  facebook, one of the biggest of the social-media giants , we find a clear signature of a change of regime that occurred in 2010 on the growth of the number of users, from a pure exponential behavior (a paradigm for unlimited growth) to a logistic function describing the evolution towards an asymptotic plateau (a paradigm for growth in competition).
Revised:  Illustrating the methodology with facebook, one of the biggest of the social-media giants . There is a clear signature of a change of regime that occurred in 2010 on the growth of the number of users, from a pure exponential behavior (a paradigm for unlimited growth) to a logistic function describing the evolution towards an asymptotic plateau (a paradigm for growth in competition).
Edit intent: clarity
Original:  Illustrating the methodology with  facebook, one of the biggest of the social-media giants , we find a clear signature of a change of regime that occurred in 2010 on the growth of the number of users, from a pure exponential behavior (a paradigm for unlimited growth) to a logistic function describing the evolution towards an asymptotic plateau (a paradigm for growth in competition).
Revised:  Illustrating the methodology with facebook, one of the biggest of the social-media giants , we find a clear signature of a change of regime that occurred in 2010 on the growth of the number of users, from a pure exponential behavior (a paradigm for unlimited growth) to a logistic function with asymptotic plateau (a paradigm for growth in competition).
Edit intent: clarity
Original:  According to our methodology, this would imply that facebook would need to increase its profit per user before the IPO by a factor of 3 to 6 in the base case scenario, 2.5 to 5 in the high growth scenario and 1.5 to 3 in the extreme growth scenario in order to meet the current, widespread, high expectations  .
Revised:  According to our methodology, this would imply that facebook would need to increase its profit per user before the IPO by a factor of 3 to 6 in the base case scenario, 2.5 to 5 in the high growth scenario and 1.5 to 3 in the extreme growth scenario in order to meet the current, widespread, high expectations . To prove the wider applicability of our methodology, the analysis is repeated on Groupon, the well-known deal-of-the-day website which is expected to go public in November 2011. The results are in line with the facebook analysis. Customer growth will plateau. By not taking this fundamental property of the growth process into consideration, estimates of its IPO are wildly overpriced .
Edit intent: meaning-changed
Original:  It is hoped that the generality and low administrative cost of this measure, which we call the Modified Greenhouse Gas Intensity measure (MGHG-INT), will eliminate any need to classify nations , and provide a uniform approach to penalizing emissions .
Revised:  It is hoped that the generality and low administrative cost of this measure, which we call the Modified Greenhouse Gas Intensity measure (MGHG-INT), will eliminate any need to classify nations .
Edit intent: coherence
Original:  The core of the MGHG-INT is what we call the Modified Gross Domestic Product ( MGDP ), based on the Inequality-adjusted Human Development Index (IHDI).
Revised:  The core of the MGHG-INT is what we call the IHDI-adjusted Gross Domestic Product ( MGDP ), based on the Inequality-adjusted Human Development Index (IHDI).
Edit intent: clarity
Original:  The core of the MGHG-INT is what we call the Modified Gross Domestic Product ( MGDP ), based on the Inequality-adjusted Human Development Index (IHDI).
Revised:  The core of the MGHG-INT is what we call the Modified Gross Domestic Product ( IDHIGDP ), based on the Inequality-adjusted Human Development Index (IHDI).
Edit intent: meaning-changed
Original:  We also propose a carbon border tax , either as a direct tax or a tax adjustment, applicable at national borders, based on MGHG-INT and MGDP . This carbon tax is supported by a proposed global Emissions Trading System (ETS) applied at the international level.
Revised:  We also propose a carbon border tax applicable at national borders, based on MGHG-INT and MGDP . This carbon tax is supported by a proposed global Emissions Trading System (ETS) applied at the international level.
Edit intent: coherence
Original:  We also propose a carbon border tax , either as a direct tax or a tax adjustment, applicable at national borders, based on MGHG-INT and MGDP . This carbon tax is supported by a proposed global Emissions Trading System (ETS) applied at the international level.
Revised:  We also propose a carbon border tax , either as a direct tax or a tax adjustment, applicable at national borders, based on MGHG-INT and IDHIGDP . This carbon tax is supported by a proposed global Emissions Trading System (ETS) applied at the international level.
Edit intent: meaning-changed
Original:  We also propose a carbon border tax , either as a direct tax or a tax adjustment, applicable at national borders, based on MGHG-INT and MGDP . This carbon tax is supported by a proposed global Emissions Trading System (ETS) applied at the international level. It is assumed that each country will implement its own equivalent carbon tax system to preserve the competitiveness of the marketplace; however, consideration of this aspect of our concept is beyond the scope of our work here.
Revised:  We also propose a carbon border tax , either as a direct tax or a tax adjustment, applicable at national borders, based on MGHG-INT and MGDP . This carbon tax is supported by a proposed global Emissions Trading System (ETS) .
Edit intent: coherence
Original:  The proposed carbon tax is analyzed in a short-term scenario with interesting outcomes, such as the simultaneous lowering of emissions levels and the maintenance of reasonable growth in MGDP. The proposed carbon tax and ETS can also be implemented at the national level in a country, in provincial or corporate slices .
Revised:  The proposed carbon tax is analyzed in a short-term scenario , where it is shown that it can result in significant reduction in global emissions while keeping the economy growing at a positive rate .
Edit intent: clarity
Original: The transient fluctuation of the population of species is investigated with a stochastic modelfor a catalytic network. The swinging changes in the fluctuation in the transient state from the initial growth to the final steady state is the consequence of a topology-dependent  competition between the catalysis and spontaneous decay.
Revised: The transient fluctuation of the population of species is investigated with an abstract stochastic model. The model describes the profit which firms make when they sell materials to a firm which produces a product and the fixed cost expense to the firms to produce those materials and product. The formulae for this model are parallel to those for population dynamics. The swinging changes in the fluctuation in the transient state from the initial growth to the final steady state is the consequence of a topology-dependent competition between the catalysis and spontaneous decay.
Edit intent: meaning-changed
Original:  The swinging changes in the fluctuation in the transient state from the initial growth to the final steady state is the consequence of a topology-dependent  competition between the catalysis and spontaneous decay. Species in a sparse random network may be more likely to become extinct than expected from the value of the limit of the fluctuation in the steady state, and there is a risk of failing to reach by far the less fluctuating steady state.
Revised:  The swinging changes in the fluctuation in the transient state from the initial growth to the final steady state is the consequence of a topology-dependent competition between the profitable interactions and expense. The firm in a sparse random network may be more likely to become extinct than expected from the value of the limit of the fluctuation in the steady state, and there is a risk of failing to reach by far the less fluctuating steady state.
Edit intent: clarity
Original:  Species in a sparse random network may be more likely to become extinct than expected from the value of the limit of the fluctuation in the steady state, and there is a risk of failing to reach by far the less fluctuating steady state.
Revised:  Species in a sparse random network economy is more likely to become extinct than expected from the value of the limit of the fluctuation in the steady state, and there is a risk of failing to reach by far the less fluctuating steady state.
Edit intent: clarity
Original:  Species in a sparse random network may be more likely to become extinct than expected from the value of the limit of the fluctuation in the steady state, and there is a risk of failing to reach by far the less fluctuating steady state.
Revised:  Species in a sparse random network may be more likely to go bankrupt than expected from the value of the limit of the fluctuation in the steady state, and there is a risk of failing to reach by far the less fluctuating steady state.
Edit intent: clarity
Original:  The financial crisis in the current and past decade has shown that one important cause of instability in global markets is the so-called financial contagion, namely the spreading of instabilities or failures of individual components of the network to other, perhaps healthier, components.
Revised:  The financial crisis in the current and past decade has shown that one important cause of instability in global markets is the so-called financial contagion, namely the spreadings of instabilities or failures of individual components of the network to other, perhaps healthier, components.
Edit intent: fluency
Original:  We formalize the homogeneous banking network model of Nier et al. and its corresponding heterogeneous version, formalize the synchronous shock propagation procedures outlined in that paper , define two appropriate stability measures and investigate the computational complexities of evaluating these measures for various network topologies and parameters of interest.
Revised:  We formalize the homogeneous banking network model of Nier et al. and its corresponding heterogeneous version, formalize the synchronous shock propagation procedures , define two appropriate stability measures and investigate the computational complexities of evaluating these measures for various network topologies and parameters of interest.
Edit intent: clarity
Original:  Analogously to the case of ordinary optimal stopping problems for one-dimensional Brow- nian motions we reduce the problem to the geometric problem of finding the smallest majorant of the reward function in an two-parameter function space.
Revised:  Analogously to the case of ordinary optimal stopping problems for one-dimensional Brownian motions we reduce the problem to the geometric problem of finding the smallest majorant of the reward function in an two-parameter function space.
Edit intent: fluency