wanyu/IteraTeR_full_sent huggingface dataset:
Original:  In this and in a companion paper (see arXiv:1103.1249 physics.soc-ph%DIFDELCMD < ]%%% ) , we employ a recently-proposed randomization method to assess in detail the role that local properties have in shaping higher-order patterns of the ITN in all its possible representations (binary/weighted, directed/undirected, aggregated/disaggregated  ) and across several years.
Revised:  In this and in a companion paper (see arXiv:1103.1249 physics.soc-ph%DIFDELCMD < ]%%% ) , we employ a recently-proposed randomization method to assess in detail the role that local properties have in shaping higher-order patterns of the ITN in all its possible representations (binary/weighted, directed/undirected, aggregated/disaggregated by commodity ) and across several years.
Edit intent: clarity
Original: In this sequel to a companion paper (see arXiv:1103.1243 physics.soc-ph%DIFDELCMD < ]%%% ) , we complement our analysis of the binary projections of the International Trade Network (ITN ) by considering its weighted representations.
Revised:  physics.soc-ph%DIFDELCMD < ]%%% ) , we complement our analysis of the binary projections of the International Trade Network (ITN ) by considering its weighted representations.
Edit intent: coherence
Original: In this sequel to a companion paper (see arXiv:1103.1243 physics.soc-ph%DIFDELCMD < ]%%% ) , we complement our analysis of the binary projections of the International Trade Network (ITN ) by considering its weighted representations.
Revised: In this sequel to a companion paper (see arXiv:1103.1243 %DIFDELCMD < ]%%% ) , we complement our analysis of the binary projections of the International Trade Network (ITN ) by considering its weighted representations.
Edit intent: meaning-changed
Original: In this sequel to a companion paper (see arXiv:1103.1243 physics.soc-ph%DIFDELCMD < ]%%% ) , we complement our analysis of the binary projections of the International Trade Network (ITN ) by considering its weighted representations.
Revised: In this sequel to a companion paper (see arXiv:1103.1243 physics.soc-ph%DIFDELCMD < ]%%% Based on the misleading expectation that weighted network properties always offer a more complete description than purely topological ones, current economic models of the International Trade Network (ITN) generally aim at explaining local weighted properties, not local binary ones. Here we complement our analysis of the binary projections of the International Trade Network (ITN ) by considering its weighted representations.
Edit intent: meaning-changed
Original: In this sequel to a companion paper (see arXiv:1103.1243 physics.soc-ph%DIFDELCMD < ]%%% ) , we complement our analysis of the binary projections of the International Trade Network (ITN ) by considering its weighted representations.
Revised: In this sequel to a companion paper (see arXiv:1103.1243 physics.soc-ph%DIFDELCMD < ]%%% ) , we complement our analysis of the binary projections of the ITN by considering its weighted representations.
Edit intent: clarity
Original:  We show that, unlike the binary case, all possible weighted representations of the ITN (directed/undirected, aggregated/disaggregated) cannot be traced back to local structural properties, which are therefore of limited informativeness.
Revised:  We show that, unlike the binary case, all possible weighted representations of the ITN (directed/undirected, aggregated/disaggregated) cannot be traced back to local country-specific properties, which are therefore of limited informativeness.
Edit intent: meaning-changed
Original:  Our results highlight that any topological property representing only partial information (e.g., degree sequences) cannot in general be obtained from the corresponding weighted property (e.g., strength sequences). Therefore the expectation that weighted structural properties offer a more complete description than purely topological ones is misleading. Our analysis of the ITN detects indirect effects that are not captured by traditional macroeconomic analyses focused only on weighted first-order country-specific properties, and highlights the limitations of models and theories that overemphasize the need to reproduce and explain such properties .
Revised:  Our two papers show that traditional macroeconomic approaches systematically fail to capture the key properties of the ITN detects indirect effects that are not captured by traditional macroeconomic analyses focused only on weighted first-order country-specific properties, and highlights the limitations of models and theories that overemphasize the need to reproduce and explain such properties .
Edit intent: clarity
Original:  Our analysis of the ITN detects indirect effects that are not captured by traditional macroeconomic analyses focused only on weighted first-order country-specific properties, and highlights the limitations of models and theories that overemphasize the need to reproduce and explain such properties .
Revised:  Our analysis of the ITN . In the binary case, they do not focus on the degree sequence and hence cannot characterize or replicate higher-order properties. In the weighted case, they generally focus on the strength sequence, but the knowledge of the latter is not enough in order to understand or reproduce indirect effects .
Edit intent: meaning-changed
Original:  To enable efficient retrieval, annotation and exchange of protein-protein interaction data, proteomics community has been developing infrastructures under Proteomics Standards Initiative and IMEx consortium. However, there is presently no resource that would provide all features necessary to construct reference interaction networks in URLanisms. The recently developed iRefIndex databaseincludes interactions from most popular repositories with a standardized protein nomenclature .
Revised:  By non-redundant, we mean that the accounting of evidence for every interaction should be faithful: each independent experimental support is counted exactly once, no more, no less. While many interactions are shared among public repositories, none of them contains the complete known interactome for any URLanism. In addition, the annotations of the same experimental result by different repositories often disagree. This brings up the issue of which annotation to keep while consolidating evidences that are the same. The iRefIndex database, including interactions from most popular repositories with a standardized protein nomenclature .
Edit intent: meaning-changed
Original:  The recently developed iRefIndex databaseincludes interactions from most popular repositories with a standardized protein nomenclature . We have developed ppiTrim, a script that can process iRefIndex to produce a consolidated dataset of physical interactions for, in principle, every URLanism.
Revised:  The recently developed iRefIndex databaseincludes interactions from most popular repositories with a standardized protein nomenclature , represents a significant advance in all aspects, especially in comprehensiveness. However, iRefIndex aims to maintain all information/annotation from original sources and requires users to perform additional processing to fully achieve the aforementioned goals. To address issues with iRefIndex and to achieve our goals, we have developed ppiTrim, a script that can process iRefIndex to produce a consolidated dataset of physical interactions for, in principle, every URLanism.
Edit intent: meaning-changed
Original:  We have developed ppiTrim, a script that can process iRefIndex to produce a consolidated dataset of physical interactions for, in principle, every URLanism. For the current publication we processed only the three largest datasets: yeast, human and fruitfly. ppiTrim maps interactants to NCBI Gene IDs, deflates possibly spoke-expanded complexes and reconciles annotation labels between different source databases.
Revised:  We have developed ppiTrim, a script that can process iRefIndex to produce a consolidated dataset of physical interactions . Our script proceeds in three stages: mapping all interactants to gene identifiers and removing all undesired raw interactions, deflating potentially expanded complexes, and reconciling for each interaction the annotation labels among different source databases. As an illustration, we have processed the three URLanismal datasets: yeast, human and fruitfly. ppiTrim maps interactants to NCBI Gene IDs, deflates possibly spoke-expanded complexes and reconciles annotation labels between different source databases.
Edit intent: meaning-changed
Original:  For the current publication we processed only the three largest datasets: yeast, human and fruitfly. ppiTrim maps interactants to NCBI Gene IDs, deflates possibly spoke-expanded complexes and reconciles annotation labels between different source databases. Our results indicate that ppiTrim is able to significantly reduce the complexity of interaction datasets. URL: ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/ppiTrim/
Revised:  For the current publication we processed only the three largest datasets: yeast, human and fruitfly. While ppiTrim can resolve most apparent conflicts between different labelings, we also discovered some unresolvable disagreements mostly resulting from different annotation policies among repositories. URL: URL
Edit intent: clarity
Original:  Implications for asset returns are derived in representative agent frameworks, in both Arrow-Debreu style economies and in sequential Radner-style economies .
Revised:  A motivating application is the extension of asset pricing theory to incorporate ambiguity about volatility and possibility. The paper provides some initial steps in this direction by deriving equilibrium relations for asset returns are derived in representative agent frameworks, in both Arrow-Debreu style economies and in sequential Radner-style economies .
Edit intent: meaning-changed
Original: We formulate a model of utility for a continuous time framework that captures the decision-maker's concern with ambiguity or model uncertainty. The main novelty is in the range of model uncertainty that is accommodated. The probability measures entertained by the decision-maker are not assumed to be equivalent to a fixed reference measure and thus the model permits ambiguity about which scenarios are possible. Modeling ambiguity about volatility is a prime motivation and a major focus. A motivating application is the extension of asset pricing theory to incorporate ambiguity about volatility and possibility.
Revised: We formulate a model of utility for a continuous time framework that captures the decision-maker's concern with ambiguity about both the drift and volatility of the driving process. At a technical level, the analysis requires a significant departure from existing continuous time modeling because it cannot be done within a probability space framework. This is because ambiguity about volatility and possibility.
Edit intent: clarity
Original:  A motivating application is the extension of asset pricing theory to incorporate ambiguity about volatility and possibility. The paper provides some initial steps in this direction by deriving equilibrium relations for asset returns in a representative agent framework, by deriving hedging bounds for asset prices, and by showing the pivotal role of `state prices' in both the equilibrium and no-arbitrage analyses .
Revised:  A motivating application is the extension of asset pricing theory to incorporate ambiguity about volatility leads invariably to a set of nonequivalent priors, that is, to priors that disagree about which scenarios are possible .
Edit intent: meaning-changed
Original:   In particular, we show that the optimality of the exit time of an interval (corresponding to the "cut-loss-or-stop-gain" strategy widely adopted in stock trading ) is endogenous for problems with convex distortion functions, including ones where distortion is absent.
Revised:  We also discuss economical interpretations of the results. In particular, we show that the optimality of the exit time of an interval (corresponding to the "cut-loss-or-stop-gain" strategy widely adopted in stock trading ) is endogenous for problems with convex distortion functions, including ones where distortion is absent.
Edit intent: meaning-changed
Original:   In particular, we show that the optimality of the exit time of an interval (corresponding to the "cut-loss-or-stop-gain" strategy widely adopted in stock trading ) is endogenous for problems with convex distortion functions, including ones where distortion is absent.
Revised:  In particular, we justify several liquidation strategies widely adopted in stock trading ) is endogenous for problems with convex distortion functions, including ones where distortion is absent.
Edit intent: clarity
Original:   In particular, we show that the optimality of the exit time of an interval (corresponding to the "cut-loss-or-stop-gain" strategy widely adopted in stock trading ) is endogenous for problems with convex distortion functions, including ones where distortion is absent. We also discuss economical interpretations of the results .
Revised:  In particular, we show that the optimality of the exit time of an interval (corresponding to the "cut-loss-or-stop-gain" strategy widely adopted in stock trading , including those of "buy and hold", "cut loss or take profit", "cut loss and let profit run" and "sell on a percentage of historical high" .
Edit intent: meaning-changed
Original: We consider a square-integrable semimartingale with conditionally independent increments and symmetric jump measure, and show that its discrete realized variance dominates its quadratic variation in increasing convex order.
Revised: We consider a square-integrable semimartingale and investigate the convex order relations between its discrete, continuous and predictable quadratic variation. As the main results, we show that if the semimartingale has conditionally independent increments and symmetric jump measure, and show that its discrete realized variance dominates its quadratic variation in increasing convex order.
Edit intent: meaning-changed
Original: We  report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for DNA under a superhelical constraint .
Revised: We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for DNA under a superhelical constraint .
Edit intent: meaning-changed
Original: We  report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for DNA under a superhelical constraint .
Revised: We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for DNA under a superhelical constraint .
Edit intent: clarity
Original: We  report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for DNA under a superhelical constraint .
Revised: We report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for DNA under a superhelical constraint .
Edit intent: fluency
Original: We  report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for DNA under a superhelical constraint .
Revised: We report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of a self-consistent linearization of the Benham model for DNA under a superhelical constraint .
Edit intent: clarity
Original: We  report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for DNA under a superhelical constraint .
Revised: We report calculations of position- and size-dependent opening probabilities for bubbles in double-stranded DNA . Our results are obtained from transfer-matrix solutions of (i) the Zimm-Bragg model for unconstrained DNA and of (ii) a self-consistent linearization of the Benham model for superhelical DNA .
Edit intent: clarity
Original:  The numerical efficiency of our method allows for the analysis of entire genomes and of random sequences of corresponding length (10^6-10^9 bp). At physiological temperatures and superhelical densities, opening is strongly cooperative with average bubble sizes of %DIFDELCMD < {\cal %%% O (100-1000) bp.
Revised:  The numerical efficiency of our method allows for the analysis of entire genomes and of random sequences of corresponding length (10^6-10^9 base pairs). We show that, at physiological conditions, opening in superhelical DNA is strongly cooperative with average bubble sizes of %DIFDELCMD < {\cal %%% O (100-1000) bp.
Edit intent: clarity
Original:  At physiological temperatures and superhelical densities, opening is strongly cooperative with average bubble sizes of %DIFDELCMD < {\cal %%% O (100-1000) bp. In general, their statistics and location are dominated by sequence heterogeneity.
Revised:  At physiological temperatures and superhelical densities, opening is strongly cooperative with average bubble sizes of %DIFDELCMD < {\cal %%% O 10^2-10^3 base pairs (bp), and orders of magnitude higher than in unconstrained DNA. In heterogeneous sequences, the average degree of base-pair opening is self-averaging, while bubble localization and statistics are dominated by sequence heterogeneity.
Edit intent: meaning-changed
Original:  In general, their statistics and location are dominated by sequence heterogeneity. For genomic DNA , bubbles are frequently located directly upstream of transcription start sites.
Revised:  In general, their statistics and location are dominated by sequence disorder. Compared to random sequences with identical GC-content, genomic DNA has a significantly increased probability to open large bubbles under superhelical stress. These bubbles are frequently located directly upstream of transcription start sites.
Edit intent: meaning-changed
Original:  Taking the FTSE100 index as a case study, and working with the Haar basis, it turns out , very unsuspectedly, that the high-energy component and a fraction of the low-energy contribution, defined by most (\simeq 98 \%) of the wavelet coefficients , can be neglected for the purpose of option premium evaluation with expiration times in the range of a few days to one month.
Revised:  Taking the FTSE100 index as a case study, and working with the Haar basis, it turns out that the small scale component defined by most (\simeq 98 \%) of the wavelet coefficients , can be neglected for the purpose of option premium evaluation with expiration times in the range of a few days to one month.
Edit intent: clarity
Original:  Taking the FTSE100 index as a case study, and working with the Haar basis, it turns out , very unsuspectedly, that the high-energy component and a fraction of the low-energy contribution, defined by most (\simeq 98 \%) of the wavelet coefficients , can be neglected for the purpose of option premium evaluation with expiration times in the range of a few days to one month.
Revised:  Taking the FTSE100 index as a case study, and working with the Haar basis, it turns out , very unsuspectedly, that the high-energy component and a fraction of the low-energy contribution, defined by most (\simeq 99.6 \%) of the wavelet coefficients , can be neglected for the purpose of option premium evaluation with expiration times in the range of a few days to one month.
Edit intent: meaning-changed
Original:  Taking the FTSE100 index as a case study, and working with the Haar basis, it turns out , very unsuspectedly, that the high-energy component and a fraction of the low-energy contribution, defined by most (\simeq 98 \%) of the wavelet coefficients , can be neglected for the purpose of option premium evaluation with expiration times in the range of a few days to one month.
Revised:  Taking the FTSE100 index as a case study, and working with the Haar basis, it turns out , very unsuspectedly, that the high-energy component and a fraction of the low-energy contribution, defined by most (\simeq 98 \%) of the wavelet coefficients can be neglected for the purpose of option premium evaluation with expiration times in the range of a few days to one month.
Edit intent: fluency
Original:  Taking the FTSE100 index as a case study, and working with the Haar basis, it turns out , very unsuspectedly, that the high-energy component and a fraction of the low-energy contribution, defined by most (\simeq 98 \%) of the wavelet coefficients , can be neglected for the purpose of option premium evaluation with expiration times in the range of a few days to one month. The relevant low-energy component, which has attenuated volatility (reduction by a factor \simeq 1/10), is (i) normally distributed, (ii) long-range correlated for intraday prices and volatility, and (iii) time-reversal asymmetric. Our results indicate that the usual non-gaussian profiles of log-return distributions contain much more information than needed for option pricing, which is essentially dependent on hidden self-correlation properties of the underlying asset fluctuations .
Revised:  Taking the FTSE100 index as a case study, and working with the Haar basis, it turns out , very unsuspectedly, that the high-energy component and a fraction of the low-energy contribution, defined by most (\simeq 98 \%) of the wavelet coefficients , can be neglected for the purpose of option premium evaluation . The relevance of the hugely compressed information provided by low-pass wavelet-filtering is related to the fact that the non-gaussian profiles of log-return distributions contain much more information than needed for option pricing, which is essentially dependent on hidden self-correlation properties of the underlying asset fluctuations .
Edit intent: coherence
Original: Regulatory dynamics has mathematical descriptions in terms of rate equations for continuous variables and, after discretization of state space and time , as Boolean maps. Here we study the effects of discretization for the notion of stability. In particular, we define the stability of a Boolean state sequence in consistency with the stability  of the original continuous trajectory that has been discretized.
Revised: Regulatory dynamics has mathematical descriptions in terms of rate equations for continuous variables and, after discretization of state space and time leads to Boolean dynamics. In the latter, the distinction between stable and unstable dynamics is usually made by checking damage after flip perturbations. Here we point out that this notion of stability is incompatible with the stability of the original continuous trajectory that has been discretized.
Edit intent: meaning-changed