wanyu/IteraTeR_v2 huggingface dataset:
Original:  To probe this issue, we have developed a new analysis method for tethered particle motion (TPM) , a versatile and commonly-used in vitro single-molecule technique.
Revised:  To probe this issue, we have developed a new analysis method for tethered particle motion , a versatile and commonly-used in vitro single-molecule technique.
Edit intent: clarity
Original:  Our method, vbTPM, is based on a variational Bayes treatment of hidden Markov models.
Revised:  Our method, vbTPM, performs variational Bayesian inference in hidden Markov models.
Edit intent: clarity
Original:  It learns the number of distinct states (i.e., DNA-protein conformations) directly from TPM data with better resolution than existing methods, while easily correcting for common experimental artifacts.
Revised:  It learns the number of distinct states (i.e., DNA-protein conformations) directly from tethered particle motion data with better resolution than existing methods, while easily correcting for common experimental artifacts.
Edit intent: clarity
Original:  Studying short (roughly 100 bp) LacI-mediated loops, we are able to resolve three distinct loop structures, more than previously reported at the single molecule level .
Revised:  Studying short (roughly 100 bp) LacI-mediated loops, we provide evidence for three distinct loop structures, more than previously reported at the single molecule level .
Edit intent: clarity
Original:  Studying short (roughly 100 bp) LacI-mediated loops, we are able to resolve three distinct loop structures, more than previously reported at the single molecule level .
Revised:  Studying short (roughly 100 bp) LacI-mediated loops, we are able to resolve three distinct loop structures, more than previously reported in single-molecule studies .
Edit intent: clarity
Original: Circadian rhythms are acquired through evolution to increase the chances for survival by synchronizing to the daylight cycle.
Revised: Circadian rhythms are acquired through evolution to increase the chances for survival through synchronizing with the daylight cycle.
Edit intent: fluency
Original:  By using a succinct model , we found that simultaneous optimization of regularity and entrainability entails  inherent features of the circadian mechanism irrespective of model details .
Revised:  By using a succinct model , we found that simultaneous optimization of regularity and entrainability entails many inherent features of the circadian mechanism irrespective of model details .
Edit intent: clarity
Original:  By using a succinct model , we found that simultaneous optimization of regularity and entrainability entails  inherent features of the circadian mechanism irrespective of model details .
Revised:  By using a succinct model , we found that simultaneous optimization of regularity and entrainability entails inherent features of the circadian mechanism .
Edit intent: clarity
Original:  At the molecular level we demonstrate the role-sharing of two light inputs, phase advance and delay, as is well observed in mammals.
Revised:  At the molecular level we demonstrate the role sharing of two light inputs, phase advance and delay, as is well observed in mammals.
Edit intent: fluency
Original:  Our results indicate that circadian clocks function optimally and that a simple mathematical model can illuminate many complex phenomena observed in nature .
Revised:  Our results indicate that circadian clocks are designed optimally for reliable clockwork through evolution .
Edit intent: clarity
Original:  The algorithm is based on generalized Jacobi (Givens) rotations and has a low computational complexity, which is of the order O( d ^4) per one set of the elementary rotations for tensors of size d x d x d . If the tensor has a different shape, a Tucker compression should be applied prior to the diagonalization  .
Revised:  The algorithm has a low computational complexity, which is of the order O( d ^4) per one set of the elementary rotations for tensors of size d x d x d . If the tensor has a different shape, a Tucker compression should be applied prior to the diagonalization .
Edit intent: coherence
Original:  The algorithm is based on generalized Jacobi (Givens) rotations and has a low computational complexity, which is of the order O( d ^4) per one set of the elementary rotations for tensors of size d x d x d . If the tensor has a different shape, a Tucker compression should be applied prior to the diagonalization  .
Revised:  The algorithm is based on generalized Jacobi (Givens) rotations and has a low computational complexity, which is of the order O( d ^4) per iteration . If the tensor has a different shape, a Tucker compression should be applied prior to the diagonalization .
Edit intent: clarity
Original:  In this paper, we take advantage of the abstraction power of category theory and provide a general representation theorem for a wide class of second order functionals which are polymorphic over a class of functors.
Revised:  In this paper, we take advantage of the abstraction power of category theory and provide a general representation theorem for a wide class of second-order functionals which are polymorphic over a class of functors.
Edit intent: fluency
Original:  In the presence of spatial structure with migration between colonies we detect various regimes of the migration rate \mu for which the fixation times have different asymptotics as \alpha \to \infty.
Revised:  In the presence of spatial structure with migration between these colonies, we detect various regimes of the migration rate \mu for which the fixation times have different asymptotics as \alpha \to \infty.
Edit intent: clarity
Original:  If \mu is of order \alpha ^p , 0\leq p \leq 1, the fixation time is \sim (2 + ( 1-p)d ) \log(\alpha)/\alpha, where d is the maximum of the migration steps that are required from the colony where the beneficial allele entered to any other colony .
Revised:  If \mu is of order \alpha ^p , 0\leq p \leq 1, the fixation time is \sim (2 + ( 1-p)d ) \log(\alpha)/\alpha, where \Delta is the number of migration steps that are required from the colony where the beneficial allele entered to any other colony .
Edit intent: clarity
Original:  On the other hand, movement and space use are also greatly influenced by  interactions between animals and their environment.
Revised:  On the other hand, movement and space use are also greatly influenced by the interactions between animals and their environment.
Edit intent: fluency
Original:  Here, we construct systems of coupled step selection functions, providing a general method for inferring population-level spatial patterns from underlying individual movement and interaction processes, a key ingredient in building a statistical mechanics for ecological systems.
Revised:  Here, we construct a general method for inferring population-level spatial patterns from underlying individual movement and interaction processes, a key ingredient in building a statistical mechanics for ecological systems.
Edit intent: clarity
Original:  Complex systems of moving and interacting objects are ubiquitous in the natural and social sciences.
Revised: 1. Complex systems of moving and interacting objects are ubiquitous in the natural and social sciences.
Edit intent: coherence
Original:  Predicting their behavior  requires models that mimic these systems with sufficient accuracy, while accounting for their inherent stochasticity.
Revised:  Predicting their behavior often requires models that mimic these systems with sufficient accuracy, while accounting for their inherent stochasticity.
Edit intent: clarity
Original:   We propose such a framework, using a novel application of the {\it Earth mover's distance , also known as the Wasserstein metric {\it  .
Revised:  We propose such a framework, using a novel application of the {\it Earth mover's distance , also known as the {\it .
Edit intent: clarity
Original:   We give a scheme for testing the hypothesis that a model is an accurate description of a data set.
Revised:  3. We give a scheme for testing the hypothesis that a model is an accurate description of a data set.
Edit intent: coherence
Original:   This work provides a fundamental toolkit to assess the quality of generic movement models of complex systems, in an absolute rather than a relative sense.
Revised:  This work provides a usable toolkit to assess the quality of generic movement models of complex systems, in an absolute rather than a relative sense.
Edit intent: clarity
Original:  2. We propose such a framework, using a novel application of the %DIFDELCMD < {\it %%% Earth mover's distance , also known as the %DIFDELCMD < {\it %%% Wasserstein metric .
Revised:  2. We propose such a framework, using a novel application of the %DIFDELCMD < {\it %%% Earth mover's distance , also known as the %DIFDELCMD < {\it %%% Wasserstein metric .
Edit intent: fluency
Original: We study the complexity of functions computable by deep feedforward neural networks with piece-wise linear activations in terms of the number of regions of linearity that they have.
Revised: We study the complexity of functions computable by deep feedforward neural networks with piecewise linear activations in terms of the number of regions of linearity that they have.
Edit intent: fluency
Original: We study the complexity of functions computable by deep feedforward neural networks with piece-wise linear activations in terms of the number of regions of linearity that they have.
Revised: We study the complexity of functions computable by deep feedforward neural networks with piece-wise linear activations in terms of the symmetries and the number of linear regions that they have.
Edit intent: clarity
Original:  Deep networks are able to sequentially map portions of each layer's input space to the same output.
Revised:  Deep networks are able to sequentially map portions of each layer's input-space to the same output.
Edit intent: fluency
Original:  In this way, deep models compute functions with a compositional structure that is able to re-use pieces of computation exponentially often in terms of their depth.
Revised:  In this way, deep models compute functions with a compositional structure that is able to re-use pieces of computation exponentially often in terms of the network's depth.
Edit intent: clarity
Original:  This note investigates the complexity of such compositional maps and contributes new theoretical results regarding the advantage of depth for neural networks with piece-wise linear activation functions  .
Revised:  This paper investigates the complexity of such compositional maps and contributes new theoretical results regarding the advantage of depth for neural networks with piece-wise linear activation functions .
Edit intent: clarity
Original:  This note investigates the complexity of such compositional maps and contributes new theoretical results regarding the advantage of depth for neural networks with piece-wise linear activation functions  .
Revised:  This note investigates the complexity of such compositional maps and contributes new theoretical results regarding the advantage of depth for neural networks with piecewise linear activation functions .
Edit intent: fluency
Original:  Reverberations in a physiologically realistic model with various physical connection topologies (from random to scale-free) have been simulated to study the effectiveness of the core-pattern method in the reconstruction of network topology from network dynamics.
Revised:  Reverberations in a physiologically realistic model with various physical connection topologies (from random to scale-free) have been simulated to study the effectiveness of the pattern-matching method in the reconstruction of network topology from network dynamics.
Edit intent: clarity
Original:  However, the core-pattern method can be effective in identifying hubs in the network.
Revised:  However, the pattern-matching method can be effective in identifying hubs in the network.
Edit intent: clarity
Original:  Since the form of reverberations are quite different for networks with and without hubs, the form of reverberations together with the reconstruction by core patterns might provide a reliable method to detect hubs in neuronal cultures.
Revised:  Since the form of reverberations are quite different for networks with and without hubs, the form of reverberations together with the reconstruction by repeating spike patterns might provide a reliable method to detect hubs in neuronal cultures.
Edit intent: clarity
Original:  and combining them with properties of the conjugate gradient algorithm,  leads to uncertainty-calibrated methods that have very limited cost overhead over conjugate gradients, a self-contained novel interpretation of the quasi-Newton and conjugate gradient algorithms, and a foundation for new nonlinear optimization methods.
Revised:  and combining them with properties of the conjugate gradient algorithm, this leads to uncertainty-calibrated methods that have very limited cost overhead over conjugate gradients, a self-contained novel interpretation of the quasi-Newton and conjugate gradient algorithms, and a foundation for new nonlinear optimization methods.
Edit intent: coherence
Original:  and combining them with properties of the conjugate gradient algorithm,  leads to uncertainty-calibrated methods that have very limited cost overhead over conjugate gradients, a self-contained novel interpretation of the quasi-Newton and conjugate gradient algorithms, and a foundation for new nonlinear optimization methods.
Revised:  and combining them with properties of the conjugate gradient algorithm, leads to uncertainty-calibrated methods with very limited cost overhead over conjugate gradients, a self-contained novel interpretation of the quasi-Newton and conjugate gradient algorithms, and a foundation for new nonlinear optimization methods.
Edit intent: fluency
Original:  We initiate the study of graph classes of %DIFDELCMD < {\it %%% power-bounded clique-width . A graph class issaid to be of power-bounded clique-width if there exists an integer k such that the k-th powers of graphs in the class form a class of bounded clique-width .
Revised:  We initiate the study of graph classes of %DIFDELCMD < {\it %%% power-bounded clique-width . A graph class issaid to be of power-bounded clique-width if there exists an integer k such that the k-th powers of the graphs are of clique-width .
Edit intent: clarity
Original:  Based on this condition , we characterize graph classes of power-bounded clique-width among classes defined by  two connected forbidden induced subgraphs.
Revised:  Based on this condition , we characterize graph classes of power-bounded clique-width within classes defined by two connected forbidden induced subgraphs.
Edit intent: clarity
Original:  We also show that for every  integer k, there exists a graph class of power-bounded clique-width such that the k-th powers of graphs in the class form a class of unbounded clique-width  .
Revised:  We also show that for every integer k, there exists a graph class of power-bounded clique-width such that the k-th powers of graphs in the class form a class of bounded clique-width .
Edit intent: clarity
Original:  While it is known that the allelic spectrum is not sufficient to infer the population size history, the distribution of coalescence times is.
Edit intent: coherence
Original:  Here we provide tight bounds on the amount of information needed to recover the population size history  at a certain level of accuracy assuming data given either by exact coalescence times, or given blocks of non-recombinant DNA sequences whose loci have approximately equal times to coalescence.
Revised:  Here we provide tight bounds on the amount of exact coalescence time data needed to recover the population size history at a certain level of accuracy assuming data given either by exact coalescence times, or given blocks of non-recombinant DNA sequences whose loci have approximately equal times to coalescence.
Edit intent: clarity
Original:  We provide lower and upper bounds (absolute or asymptotic in the number of vertices) on the maximum possible chromatic number in the following classes of graphs with bounded clique number : * rectangle overlap graphs -
Revised:  We provide lower and upper bounds (absolute or asymptotic in the number of graphs with bounded clique number : * rectangle overlap graphs -
Edit intent: clarity
Original: - overlap graphs of axis-aligned rectangles in the plane, * subtree overlap graphs -- overlap graphs of subtrees of a tree, * interval filament graphs -- intersection graphs of continuous non-negative functions defined on closed intervals with value zero on the endpoints, a subclass of subtree overlap graphs.
Revised: - overlap graphs of axis-aligned rectangles in the plane, * subtree overlap graphs , and interval filament graphs -- intersection graphs of continuous non-negative functions defined on closed intervals with value zero on the endpoints, a subclass of subtree overlap graphs.
Edit intent: clarity
Original:  We also introduce a concept of K_k-free colorings and show that for some geometric representations, the K_3-free chromatic number can be bounded in terms of the clique number although the ordinary (K_2-free) chromatic number cannot.
Revised:  We also introduce a concept of K_k-free colorings and show that for some geometric representations, K_3-free chromatic number can be bounded in terms of the clique number although the ordinary (K_2-free) chromatic number cannot.
Edit intent: fluency
Original:  We also introduce a concept of K_k-free colorings and show that for some geometric representations, the K_3-free chromatic number can be bounded in terms of the clique number although the ordinary (K_2-free) chromatic number cannot.
Revised:  We also introduce a concept of K_k-free colorings and show that for some geometric representations, the K_3-free chromatic number can be bounded in terms of clique number although the ordinary (K_2-free) chromatic number cannot.
Edit intent: fluency
Original:  However, in the interim the rate at which electric vehicles can be deployed will depend on our ability to charge these vehicles in a timely manner .
Revised:  However, in the interim the rate at which electric vehicles can be deployed will depend on our ability to charge these vehicles without inconveniencing their owners .
Edit intent: clarity
Original:  In this paper, we investigate  fairness mechanisms to distribute power to electric vehicles on a smart grid.
Revised:  In this paper, we investigate using fairness mechanisms to distribute power to electric vehicles on a smart grid.
Edit intent: clarity
Original:  However, when we can use reliable information on departure times and driving distances for the electric vehicles, we can reduce the delays to a few minutes  when the capacity available for charging  exceeds their requirements by as little as 5\%.
Revised:  However, when we can use reliable information on departure times and driving distances for the electric vehicles, we can reduce the delays to a few minutes , even when the capacity available for charging exceeds their requirements by as little as 5\%.
Edit intent: coherence
Original:  However, when we can use reliable information on departure times and driving distances for the electric vehicles, we can reduce the delays to a few minutes  when the capacity available for charging  exceeds their requirements by as little as 5\%.
Revised:  However, when we can use reliable information on departure times and driving distances for the electric vehicles, we can reduce the delays to a few minutes when the capacity available for charging electric vehicles exceeds their requirements by as little as 5\%.
Edit intent: fluency
Original: In this paper we provide two representations for stochastic ion channel kinetics, and compare the performance of exact simulation strategies with different, commonly used , approximate strategies .
Revised: In this paper we provide two representations for stochastic ion channel kinetics, and compare the performance of exact simulation with a commonly used numerical approximation strategy .
Edit intent: clarity
Original:  We perform a thorough computational complexity study of the problem on subclasses of perfect graphs and thereby identify several polynomial-time solvable cases for interval graphs, among others .
Revised:  We perform a thorough computational complexity study of the problem on subclasses of perfect graphs and identify several polynomial-time solvable cases for interval graphs, among others .
Edit intent: coherence
Original: The partition of graphs into nice subgraphs is a central algorithmic problem with strong ties to matching theory.
Revised: The partition of graphs into "nice" subgraphs is a central algorithmic problem with strong ties to matching theory.
Edit intent: fluency
Original:  We perform a thorough computational complexity study of the problem on subclasses of perfect graphs and identify several polynomial-time solvable and NP-hard cases, for example, on interval graphs , grid graphs, and bipartite permutation graphs.
Revised:  We perform a thorough computational complexity study of the problem on subclasses of perfect graphs and identify several polynomial-time solvable cases, for example, on interval graphs , grid graphs, and bipartite permutation graphs.
Edit intent: clarity
Original: In a discrete-time market, we study the problem of model-independent superhedging of exotic options under portfolio constraints.
Revised: In a discrete-time market, we study model-independent superhedging of exotic options under portfolio constraints.
Edit intent: clarity
Original: In order to compensate for the higher cost of double double and quad double arithmetic when solving large polynomial systems, we investigate the application of NVIDIA Tesla C2050, K20C , and K40 general purpose graphics processing units.
Revised: In order to compensate for the higher cost of double double and quad double arithmetic when solving large polynomial systems, we investigate the application of NVIDIA Tesla C2050, K20C general purpose graphics processing units.
Edit intent: clarity
Original: Background: Interleukin-2 receptor antagonists (IL-2RA) are frequently used as induction therapy in liver transplant recipients to decrease the risk of acute rejection while allowing the reduction of concomitant immunosuppression.
Revised:  Interleukin-2 receptor antagonists (IL-2RA) are frequently used as induction therapy in liver transplant recipients to decrease the risk of acute rejection while allowing the reduction of concomitant immunosuppression.
Edit intent: coherence
Original:  Methods: We performed a systematic literature search for relevant studies.
Revised:  We performed a systematic literature search for relevant studies.
Edit intent: coherence
Original:  Results: Six studies (2 randomized and 4 nonrandomized) met the elegibility criteria.
Revised:  Six studies (2 randomized and 4 nonrandomized) met the elegibility criteria.
Edit intent: clarity
Original:  Acute rejection at 6 months or later favored the use of IL-2RA significantly (relative risk RR 0.38;
Revised:  Acute rejection at 6 months or later favored the use of IL-2RA significantly (relative risk (RR) 0.38;
Edit intent: clarity
Original:  95\% confidence interval CI 0.22-0.66, p-value p = 0.0005).
Revised:  95\% confidence interval (CI) 0.22-0.66, p-value p = 0.0005).
Edit intent: clarity
Original:  95\% confidence interval CI 0.22-0.66, p-value p = 0.0005).
Revised:  95\% confidence interval CI 0.22-0.66, p = 0.0005).
Edit intent: clarity
Original:  95\% confidence interval CI 0.22-0.66, p-value p = 0.0005).
Revised:  95\% confidence interval CI 0.22-0.66, p-value p = 0.0005).
Edit intent: fluency
Original:  Conclusions: The use of IL-2RA is safe and is associated with a statistically significantly lower incidence of acute rejection after transplantation and substantial reduction of steroid-resistant rejection, graft loss and patient death.
Revised:  The use of IL-2RA is safe and is associated with a statistically significantly lower incidence of acute rejection after transplantation and substantial reduction of steroid-resistant rejection, graft loss and patient death.
Edit intent: coherence