wanyu/IteraTeR_full_sent huggingface dataset:
Original:  Available techniques, ranging from simple automated docking procedures to sophisticated thermodynamics-based methods, have been developed almost exclusively for use in soluble proteins . Here we extend the asymptotically exact Alchemical Free Energy Perturbation technique to quantifying occupancies of sites on proteins in a complex bulk, including phase-separated, anisotropic, or non-dilute solutions, using a thermodynamically consistent and easily generalized approach that resolves several previous ambiguities .
Revised:  Available techniques, ranging from simple automated docking procedures to sophisticated thermodynamics-based methods, have been developed with soluble proteins in mind. Biologically and pharmacologically relevant protein-ligand interactions often occur in complex environments, including lamellar phases like membranes and crowded, non-dilute solutions. Here we revisit the theoretical bases of ligand binding equilibria, avoiding overly specific assumptions that are nearly always made when describing receptor-ligand binding. Building on this formalism, we extend the asymptotically exact Alchemical Free Energy Perturbation technique to quantifying occupancies of sites on proteins in a complex bulk, including phase-separated, anisotropic, or non-dilute solutions, using a thermodynamically consistent and easily generalized approach that resolves several previous ambiguities .
Edit intent: meaning-changed
Original:  Here we extend the asymptotically exact Alchemical Free Energy Perturbation technique to quantifying occupancies of sites on proteins in a complex bulk, including phase-separated, anisotropic, or non-dilute solutions, using a thermodynamically consistent and easily generalized approach that resolves several previous ambiguities .
Revised:  Here we extend the asymptotically exact Alchemical Free Energy Perturbation technique to quantifying occupancies of sites on proteins in a complex bulk, including phase-separated, anisotropic, or non-dilute solutions, using a thermodynamically consistent and easily generalized approach that resolves several ambiguities of current frameworks .
Edit intent: clarity
Original:  We apply this approach to calculate the likelihood that  cholesterol binds to widely-studied crystallographic sites on 3 GPCRs (beta2-adrenergic, 5HT-2B, and mu-opioid) at a range of concentrations.
Revised:  We apply this approach to compute the likelihood that cholesterol binds to widely-studied crystallographic sites on 3 GPCRs (beta2-adrenergic, 5HT-2B, and mu-opioid) at a range of concentrations.
Edit intent: fluency
Original:  We apply this approach to calculate the likelihood that  cholesterol binds to widely-studied crystallographic sites on 3 GPCRs (beta2-adrenergic, 5HT-2B, and mu-opioid) at a range of concentrations.
Revised:  We apply this approach to calculate the likelihood that membrane cholesterol binds to widely-studied crystallographic sites on 3 GPCRs (beta2-adrenergic, 5HT-2B, and mu-opioid) at a range of concentrations.
Edit intent: meaning-changed
Original:  We apply this approach to calculate the likelihood that  cholesterol binds to widely-studied crystallographic sites on 3 GPCRs (beta2-adrenergic, 5HT-2B, and mu-opioid) at a range of concentrations.
Revised:  We apply this approach to calculate the likelihood that cholesterol binds to known crystallographic sites on 3 GPCRs (beta2-adrenergic, 5HT-2B, and mu-opioid) at a range of concentrations.
Edit intent: clarity
Original:  We apply this approach to calculate the likelihood that  cholesterol binds to widely-studied crystallographic sites on 3 GPCRs (beta2-adrenergic, 5HT-2B, and mu-opioid) at a range of concentrations.
Revised:  We apply this approach to calculate the likelihood that cholesterol binds to widely-studied crystallographic sites on 3 GPCRs at a range of concentrations.
Edit intent: coherence
Original:  We provide conditions under which group membership is estimated consistently and establish asymptotic normality of the resulting estimators. 
Revised:  We provide conditions under which group membership is estimated consistently and establish asymptotic normality of the resulting estimators. Simulations show that the method works well in finite samples when T is reasonably large. To illustrate the proposed methodology we study the effects of the adoption of Right-to-Carry concealed weapon laws on violent crime rates using panel data of 51 U.S. states from 1977 - 2010.
Edit intent: meaning-changed
Original:  We analyze the economic diversification paths of 93 countries between 1970 and 2010 and find that countries enter unrelated products in only about 7.2\% of all observations.
Revised:  We analyze the economic diversification paths of 93 countries between 1965 and 2014 and find that countries enter unrelated products in only about 7.2\% of all observations.
Edit intent: meaning-changed
Original:  The data shows that countries that enter more unrelated activities experience an increase in short-term economic growthof 0.5\% per annum compared to those with similar levels of income, human capital, capital stock per worker, and economic complexity.
Revised:  The data shows that countries that enter more unrelated activities experience a small but significant increase in future economic growth, compared to countries with a similar level of income, human capital, capital stock per worker, and economic complexity.
Edit intent: meaning-changed
Original: Permutation relative entropy is proposed to quantify time irreversibilityin our nonlinear dynamics analysis of electroencephalogram (EEG). Ordinal patterns in multi-dimension phase space of time series are symbolized, and the probabilistic divergences of all symmetric ordinal pairs are measured by relative entropy as time irreversibility.
Revised: To simplify the quantification of time irreversibility, we employ order patterns instead of the raw multi-dimension phase space of time series are symbolized, and the probabilistic divergences of all symmetric ordinal pairs are measured by relative entropy as time irreversibility.
Edit intent: meaning-changed
Original:  Ordinal patterns in multi-dimension phase space of time series are symbolized, and the probabilistic divergences of all symmetric ordinal pairs are measured by relative entropy as time irreversibility.
Revised:  Ordinal patterns in multi-dimension vectors in time series, and considering the existence of forbidden permutation, we propose a subtraction-based parameter, Ys, to measure the probabilistic differences between symmetric permutations for time series are symbolized, and the probabilistic divergences of all symmetric ordinal pairs are measured by relative entropy as time irreversibility.
Edit intent: meaning-changed
Original:  Analyzing multi-channel EEG from 18 healthy volunteers and 18 epileptic patients (all in their seize-free intervals), the derived relative entropy of symmetrical ordinal patterns shows advantages to other time irreversible parameters and significantly distinguish two kinds of brain electric signals (the epileptic have lower temporal asymmetries than the healthy) .
Revised:  Two chaotic models, the logistic and Henon systems, and reversible Gaussian process and their surrogate data are used to validate the time-irreversible measure, and time irreversibility of epileptic EEGs from Nanjing General Hospital is detected by the parameter .
Edit intent: meaning-changed
Original:  Test results prove that it is effective to quantity time irreversibility by measuring probabilistic divergence of symmetrical ordinal patternsand validate our hypothesis that epilepsy has lasting impacts on brain' nonlinear dynamics, leading to a decline in brain signals directional asymmetry or time irreversibility, and the losing temporal asymmetries stemming from our findings may contribute to the preclinical diagnosis of epilepsy .
Revised:  Test results prove that it is promising to quantify time irreversibility by measuring probabilistic divergence of symmetrical ordinal patternsand validate our hypothesis that epilepsy has lasting impacts on brain' nonlinear dynamics, leading to a decline in brain signals directional asymmetry or time irreversibility, and the losing temporal asymmetries stemming from our findings may contribute to the preclinical diagnosis of epilepsy .
Edit intent: clarity
Original:  Test results prove that it is effective to quantity time irreversibility by measuring probabilistic divergence of symmetrical ordinal patternsand validate our hypothesis that epilepsy has lasting impacts on brain' nonlinear dynamics, leading to a decline in brain signals directional asymmetry or time irreversibility, and the losing temporal asymmetries stemming from our findings may contribute to the preclinical diagnosis of epilepsy .
Revised:  Test results prove that it is effective to quantity time irreversibility by measuring the subtraction-based probabilistic differences between symmetric order patterns, and our findings highlight the manifestation of nonlinearity of whether healthy or diseased EEGs and suggest that the epilepsy leads to a decline in brain signals directional asymmetry or time irreversibility, and the losing temporal asymmetries stemming from our findings may contribute to the preclinical diagnosis of epilepsy .
Edit intent: meaning-changed
Original:  Test results prove that it is effective to quantity time irreversibility by measuring probabilistic divergence of symmetrical ordinal patternsand validate our hypothesis that epilepsy has lasting impacts on brain' nonlinear dynamics, leading to a decline in brain signals directional asymmetry or time irreversibility, and the losing temporal asymmetries stemming from our findings may contribute to the preclinical diagnosis of epilepsy .
Revised:  Test results prove that it is effective to quantity time irreversibility by measuring probabilistic divergence of symmetrical ordinal patternsand validate our hypothesis that epilepsy has lasting impacts on brain' nonlinear dynamics, leading to a decline in the nonlinearity of brain electrical activities during seize-free intervals .
Edit intent: clarity
Original:  Compatible with the architecture of cortical neural networks, traveling waves emerge in two-population networks of excitatory and inhibitory neurons as a combination of delay-induced temporal oscillations and spatial oscillations due to distance-dependent connectivity profiles.
Revised:  Compatible with the architecture of cortical neural networks, wave trains emerge in two-population networks of excitatory and inhibitory neurons as a combination of delay-induced temporal oscillations and spatial oscillations due to distance-dependent connectivity profiles.
Edit intent: clarity
Original:  While these networks provide global connectivity and sustain the broad spectrum of the functions of the brain, the underlying routing strategies for communication between the different areas and their control remain to be elucidated. Here, we investigate the flow of information in connectomes of several species using greedy routing as a distributed navigation protocol .
Revised:  Using a decentralized navigation protocol, we investigate the relationship between the structure of the connectomes of different species and their spatial layout. As a navigation strategy, we use greedy routing where nearest neighbors, in terms of geometric distance, are visited. We measure the fraction of successful greedy paths and their length as compared to shortest paths in the topology of connectomes .
Edit intent: meaning-changed
Original:  In Euclidean space, in which brains have evolved, our results unveil that the navigability of brains vary highly across species. On the one hand, this result may suggest that the more evolved URLanism is, the more the structure of the connectome is encoded in the URLanization of the brain.
Revised:  In Euclidean space, in which brains have evolved, our results unveil that the navigability of their connectomes. In contrast, we find that hyperbolic space, the connectome is encoded in the URLanization of the brain.
Edit intent: meaning-changed
Original:  On the one hand, this result may suggest that the more evolved URLanism is, the more the structure of the connectome is encoded in the URLanization of the brain. On the other hand, conclusions obtained using coarse-grained connectomes, where nodes correspond to areas instead of individual neurones, may not apply to connectomes obtained at the microscopic, neuronal level. Moreover, we prove that the effective geometry of the brain is better described as hyperbolic rather than Euclidean.
Revised:  On the one hand, this result may suggest that the more evolved URLanism is, the more the structure of the effective geometry of the brain is better described as hyperbolic rather than Euclidean.
Edit intent: clarity
Original:  Moreover, we prove that the effective geometry of the brain is better described as hyperbolic rather than Euclidean. This indicates that other factors besides degrees and Euclidean distance play a significant role in the existence of connections. On a more practical perspective, hyperbolic embeddings offer a universal and meaningful representations to compare brain networks across species on an equal footing.
Revised:  Moreover, we prove that the effective geometry of complex networks, provides almost perfectly navigable maps of connectomes for all species, meaning that hyperbolic distances are exceptionally congruent with the structure of connectomes. Hyperbolic maps therefore offer a quantitative meaningful representation of connectomes that suggests a new cartography of the brain based on the combination of its connectivity with its effective geometry rather than on its anatomy only. Hyperbolic maps also provide a universal framework to study decentralized communication processes in connectomes of different species and at different scales on an equal footing.
Edit intent: coherence
Original:  We derive the test statistic, study the size and power properties of the test , and demonstrate its implementation with intraday stock market return data. The test has conservative size properties and good power to detect varying variance and unit root in the presence of varying variance .
Revised:  We derive the test statistic, study the size and power properties of the test , and demonstrate its application using 137Cs gamma ray decay data. Future areas of research include testing for strict stationarity of graph signals, with applications in learning convolutional neural networks on graphs, denoising, and inpainting .
Edit intent: meaning-changed
Original:  This somewhat counter-intuitive observation, referred to as {\em paradox of codependence is inconsistent with the existing paradigm of a mechanistic tug-of-war between oppositely directed motors.
Revised:  This counter-intuitive observation, referred to as {\em paradox of codependence is inconsistent with the existing paradigm of a mechanistic tug-of-war between oppositely directed motors.
Edit intent: coherence
Original:  Incorporating this catchbonding behavior of dynein in a theoretical model and using experimentally relevant measures characterizing cargo transport , we show that the functional divergence of the two motors species manifests itself as an internal regulatory mechanism for bidirectional transport and resolves the paradox of codependence.
Revised:  Incorporating this catchbonding behavior of dynein in a theoretical model , we show that the functional divergence of the two motors species manifests itself as an internal regulatory mechanism for bidirectional transport and resolves the paradox of codependence.
Edit intent: coherence
Original:  Incorporating this catchbonding behavior of dynein in a theoretical model and using experimentally relevant measures characterizing cargo transport , we show that the functional divergence of the two motors species manifests itself as an internal regulatory mechanism for bidirectional transport and resolves the paradox of codependence. Our model reproduces the key experimental features in appropriate parameter regimes and provides an unifying framework for bidirectional cargo transport .
Revised:  Incorporating this catchbonding behavior of dynein in a theoretical model and using experimentally relevant measures characterizing cargo transport , we show that the functional divergence of the two motors species manifests itself as an internal regulatory mechanism , and leads to codependent transport behaviour in biologically relevant regimes. Using analytical methods and stochastic simulations, we analyse the processivity characteristics and probability distribution of run times and pause times of transported cellular cargoes. We show that catchbonding can drastically alter the transport characteristics and also provide a plausible resolution of the paradox of codependence .
Edit intent: meaning-changed
Original:  We also find that , when wealth is required to satisfy the no-bankruptcy constraint, the boundedness assumption can be dropped provided that we impose a certain integrability condition , related to some strengthened form of no-arbitrage.
Revised:  We also find that , when wealth is required to satisfy the no-bankruptcy constraint, the boundedness assumption can be dropped provided that we impose suitable integrability conditions , related to some strengthened form of no-arbitrage.
Edit intent: clarity
Original: Based on endogenous economic growth models and the panel data of 31 regions in China, this paper explores the following four questions: Do spatial knowledge spillovers among regions exist ? Do spatial knowledge spillovers promote regional innovative activities ?
Revised: This paper extends endogenous economic growth models and the panel data of 31 regions in China, this paper explores the following four questions: Do spatial knowledge spillovers among regions exist ? Do spatial knowledge spillovers promote regional innovative activities ?
Edit intent: meaning-changed
Original: Based on endogenous economic growth models and the panel data of 31 regions in China, this paper explores the following four questions: Do spatial knowledge spillovers among regions exist ? Do spatial knowledge spillovers promote regional innovative activities ?
Revised: Based on endogenous economic growth models and the panel data of 31 regions in China, this paper explores the following four questions: Do spatial knowledge spillovers among regions exist , whether spatial knowledge spillovers promote regional innovative activities ?
Edit intent: coherence
Original: Based on endogenous economic growth models and the panel data of 31 regions in China, this paper explores the following four questions: Do spatial knowledge spillovers among regions exist ? Do spatial knowledge spillovers promote regional innovative activities ? What is the radiation range of spatial knowledge spillovers? Do external knowledge spillovers affect the evolution of regional innovations in the long run ?
Revised: Based on endogenous economic growth models and the panel data of 31 regions in China, this paper explores the following four questions: Do spatial knowledge spillovers among regions exist ? Do spatial knowledge spillovers promote regional innovative activities , and whether external knowledge spillovers affect the evolution of regional innovations in the long run ?
Edit intent: coherence
Original:  Do external knowledge spillovers affect the evolution of regional innovations in the long run ? The results show that spatial knowledge spillovers exist, and though the range of knowledge spillover is within 1000 kilometers in China, it pushes up regional innovative activities. Moreover, since developing regions benefit more from external knowledge spillovers than developed regions , it leads to the convergence of regional knowledge growth rate .
Revised:  Do external knowledge spillovers affect the evolution of regional innovations in the long run . We empirically verify the theoretical results through applying spatial statistics and econometric model in the analysis of panel data of 31 regions in China. An accurate estimate of the range of knowledge spillovers is achieved and the convergence of regional knowledge growth rate is found, with clear evidences that developing regions benefit more from external knowledge spillovers than developed regions , it leads to the convergence of regional knowledge growth rate .
Edit intent: meaning-changed
Original:  This approach is applied to solve several drug design problems, including generation of compounds containing a given scaffold, generation of compounds with specific drug-likeness and synthetic accessibility requirements, as well as generating dual inhibitors against JNK3 and GSK3b.
Revised:  This approach is applied to solve several drug design problems, generation of compounds containing a given scaffold, generation of compounds with specific drug-likeness and synthetic accessibility requirements, as well as generating dual inhibitors against JNK3 and GSK3b.
Edit intent: coherence
Original:  In this work, a new de novo molecular design framework is proposed based on a sequential graph generator . Compared with previous graph generative models, the proposed method is much more tuned for molecule generation and have been scaled up to cover significantly larger molecules in the ChEMBL database.
Revised:  In this work, a new de novo molecular design framework is proposed based on a type sequential graph generators that do not use atom level recurrent units . Compared with previous graph generative models, the proposed method is much more tuned for molecule generation and have been scaled up to cover significantly larger molecules in the ChEMBL database.
Edit intent: meaning-changed
Original:  This approach is applied to solve several drug design problems,  generation of compounds containing a given scaffold, generation of compounds with specific drug-likeness and synthetic accessibility requirements, as well as generating dual inhibitors against JNK3 and GSK3b . Results show high enrichment rates for outputs satisfying the given requirements.
Revised:  This approach is applied to solve several drug design problems, including the generation of compounds containing a given scaffold, generation of compounds with specific drug-likeness and synthetic accessibility requirements, as well as generating dual inhibitors against JNK3 and GSK3b . Results show high enrichment rates for outputs satisfying the given requirements.
Edit intent: clarity
Original:  This approach is applied to solve several drug design problems,  generation of compounds containing a given scaffold, generation of compounds with specific drug-likeness and synthetic accessibility requirements, as well as generating dual inhibitors against JNK3 and GSK3b . Results show high enrichment rates for outputs satisfying the given requirements.
Revised:  This approach is applied to solve several drug design problems, generation of compounds containing a given scaffold, generation of compounds with specific drug-likeness and synthetic accessibility requirements, as well as generating dual inhibitors against JNK3 and GSK3\beta . Results show high enrichment rates for outputs satisfying the given requirements.
Edit intent: meaning-changed
Original: Given a set S of n d-dimensional points  , the k-nearest neighbors ( KNN) is the problem of quickly finding k points in S that are nearest to a query point q.
Revised: In machine learning, classifiers are used to predict a class of a given query based on an existing (classified) database. Given a database S of n d-dimensional points , the k-nearest neighbors ( KNN) is the problem of quickly finding k points in S that are nearest to a query point q.
Edit intent: meaning-changed