wanyu/IteraTeR_v2 huggingface dataset:
Original:  Here, we built a set of mathematical models of mRNA-miRNA interactions and systematically analyzed their dynamical responses under various conditions.
Revised:  Here, we built a set of mathematical models of mRNA-miRNA interactions and systematically analyzed the sensitivity of response curves under various conditions.
Edit intent: clarity
Original:  Last, multiple miRNA binding sites  on a target mRNA leads to emergence of nonmonotonic dual response (duality) and bistability even in the absence of any imposed feedback regulation .
Revised:  Last, multiple miRNA binding sites exist on a target mRNA leads to emergence of nonmonotonic dual response (duality) and bistability even in the absence of any imposed feedback regulation .
Edit intent: clarity
Original:  Last, multiple miRNA binding sites  on a target mRNA leads to emergence of nonmonotonic dual response (duality) and bistability even in the absence of any imposed feedback regulation .
Revised:  Last, multiple miRNA binding sites on a target mRNA .
Edit intent: clarity
Original:  Thus, we demonstrated several novel functionalities that can be generated from simple mRNA-miRNA reciprocal regulation , in addition to canonical miRNA mediated degradation and translational repression of mRNA. Quantitative experiments are suggested to test the model predictions .
Revised:  Thus, we demonstrated several novel functionalities that can be generated from simple mRNA-miRNA reciprocal regulation in cell fate decision .
Edit intent: clarity
Original:  Using this model, we study the performance of a typical D2D receiver in terms of coverage probability under two realistic content availability setups: (i) content of interest for a typical device is available at a device chosen uniformly at random from the same cluster, which we term uniform content availability , and (ii) content of interest is available at the k^{th} closest device from the typical device inside the same cluster, which we term k-closest content availability .
Revised:  Using this model, we study the performance of a typical D2D receiver in terms of coverage probability under two realistic content availability setups: (i) content of interest for a typical device is available at a device chosen uniformly at random from the same cluster, which we term uniform content availability , and (ii) content of interest is available at the k^{th} closest device from the typical device inside the same cluster, which we term k-closest content availability .
Edit intent: fluency
Original:  Using these coverage probability results, we also characterize the area spectral efficiency ( \mathtt{ASE ) of the whole network for the two setups.
Revised:  Using these coverage probability results, we also characterize the area spectral efficiency ( ASE ) of the whole network for the two setups.
Edit intent: coherence
Original:  Our analysis reveals that an optimum number of D2D transmitters must be simultaneously activated per cluster in order to maximize \mathtt{ASE . This can be interpreted as the classical tradeoff between more aggressive frequency reuse and higher interference power.
Revised:  Our analysis reveals that an optimum number of D2D transmitters must be simultaneously activated per cluster in order to maximize ASE . This can be interpreted as the classical tradeoff between more aggressive frequency reuse and higher interference power.
Edit intent: fluency
Original:  The optimum number of simultaneously transmitting devices and the resulting \mathtt{ASE increase as the content is made available closer to the receivers.
Revised:  The optimum number of simultaneously transmitting devices and the resulting ASE increase as the content is made available closer to the receivers.
Edit intent: fluency
Original:  Our analysis also quantifies the best and worst case performance of clustered D2D networks both in terms of coverage and \mathtt{ASE .
Revised:  Our analysis also quantifies the best and worst case performance of clustered D2D networks both in terms of coverage and ASE .
Edit intent: coherence
Original: During cell migration, cells become polarized, change their shape, and move in response to various cues, both internal and external .
Revised: During cell migration, cells become polarized, change their shape, and move in response to various internal and external .
Edit intent: clarity
Original:  To study those effects , we introduce a three-dimensional reaction-diffusion model of a cell.
Revised:  To study those effects , we introduce a 3D reaction-diffusion model of a cell.
Edit intent: fluency
Original: The Goulden-Jackson cluster method is a powerful tool for obtaining generating functions for words in free monoids by occurrences of a set of subwords.
Revised: The Goulden-Jackson cluster method is a powerful tool for obtaining generating functions for counting words in a free monoid by occurrences of a set of subwords.
Edit intent: clarity
Original:  As a sample application of the monoid network cluster method, we compute bivariate and multivariate generating functions for Motzkin paths---both with height bounded and unbounded---by statistics corresponding to the number of occurrences of various subwords, yielding both closed-form and continued fraction formulae.
Revised:  As a sample application of the generalized cluster method, we compute bivariate and multivariate generating functions for Motzkin paths---both with height bounded and unbounded---by statistics corresponding to the number of occurrences of various subwords, yielding both closed-form and continued fraction formulae.
Edit intent: clarity
Original:  As a sample application of the monoid network cluster method, we compute bivariate and multivariate generating functions for Motzkin paths---both with height bounded and unbounded---by statistics corresponding to the number of occurrences of various subwords, yielding both closed-form and continued fraction formulae.
Revised:  As a sample application of the monoid network cluster method, we compute bivariate and multivariate generating functions counting Motzkin paths---both with height bounded and unbounded---by statistics corresponding to the number of occurrences of various subwords, yielding both closed-form and continued fraction formulae.
Edit intent: clarity
Original:  Since these distributions cannot be worked with directly, we consider approximating  by suitably defined random walks in tree-space.
Revised:  Since these distributions cannot be worked with directly, we consider approximating them by suitably defined random walks in tree-space.
Edit intent: fluency
Original:  This result opens  the possibility of statistical modelling using distributions obtained from  Brownian motion on tree-space  .
Revised:  This result opens up the possibility of statistical modelling using distributions obtained from Brownian motion on tree-space .
Edit intent: fluency
Original:  The model also includes a random damage and the possibility of several claims.
Revised:  The model includes a random damage and the possibility of several claims.
Edit intent: clarity
Original:  We find that EDS paths make more plausible  intra-protein communication pathways than the popular shortest or BFS paths.
Revised:  We find that EDS paths make more plausible intra-protein communication pathways than BFS paths.
Edit intent: clarity
Original:  We were also able to retrieve independent dynamic segments and recover hub residues identified for the receptor tyrosine kinase KIT (1T45) proteinwith information from EDS paths .
Revised:  We were also able to retrieve independent dynamic segments and recover hub residues identified for the receptor tyrosine kinase KIT protein .
Edit intent: clarity
Original: We compare paths constructed on protein residue networks via a Euclidean Distance Search algorithm called EDS, to paths found using the  Breadth First Search (BFS) method in terms of their stability, communication propensity and compressibility.
Revised: We compare paths constructed on protein residue networks via a Euclidean Distance Search (EDS) to paths found using the Breadth First Search (BFS) method in terms of their stability, communication propensity and compressibility.
Edit intent: clarity
Original: We compare paths constructed on protein residue networks via a Euclidean Distance Search algorithm called EDS, to paths found using the  Breadth First Search (BFS) method in terms of their stability, communication propensity and compressibility.
Revised: We compare paths constructed on protein residue networks via a Euclidean Distance Search algorithm called EDS, to paths found using the commonly used Breadth First Search (BFS) method in terms of their stability, communication propensity and compressibility.
Edit intent: clarity
Original:  Since EDS paths are more stable , have better communication propensity and are more compressible, we propose that they make more plausible discrete models of intra-protein communication pathways than BFS paths .
Revised:  Since EDS paths are more stable and have better communication propensity and are more compressible, we propose that they make more plausible discrete models of intra-protein communication pathways than BFS paths .
Edit intent: fluency
Original: We compare paths constructed on protein residue networks via a Euclidean Distance Search (EDS) to paths found using the commonly used Breadth First Search (BFS) method in terms of their ability to capture allosteric communication within proteins.
Revised: Paths constructed on protein residue networks via a Euclidean Distance Search (EDS) to paths found using the commonly used Breadth First Search (BFS) method in terms of their ability to capture allosteric communication within proteins.
Edit intent: coherence
Original: We compare paths constructed on protein residue networks via a Euclidean Distance Search (EDS) to paths found using the commonly used Breadth First Search (BFS) method in terms of their ability to capture allosteric communication within proteins.
Revised: We compare paths constructed on protein residue networks (PRNs) via Euclidean Distance Search (EDS) to paths found using the commonly used Breadth First Search (BFS) method in terms of their ability to capture allosteric communication within proteins.
Edit intent: clarity
Original: We compare paths constructed on protein residue networks via a Euclidean Distance Search (EDS) to paths found using the commonly used Breadth First Search (BFS) method in terms of their ability to capture allosteric communication within proteins.
Revised: We compare paths constructed on protein residue networks via a Euclidean Distance Search (EDS) are compared with paths generated by Breadth First Search (BFS) method in terms of their ability to capture allosteric communication within proteins.
Edit intent: clarity
Original: We compare paths constructed on protein residue networks via a Euclidean Distance Search (EDS) to paths found using the commonly used Breadth First Search (BFS) method in terms of their ability to capture allosteric communication within proteins.
Revised: We compare paths constructed on protein residue networks via a Euclidean Distance Search (EDS) to paths found using the commonly used Breadth First Search (BFS) in terms of their ability to capture allosteric communication within proteins.
Edit intent: clarity
Original: Paths constructed on protein residue networks (PRNs) via Euclidean Distance Search (EDS) are compared with paths generated by Breadth First Search (BFS) in terms of their ability to capture key features of allosteric communication in a type III receptor tyrosine kinase (KIT).
Revised: Although proteins have been recognized as small-world networks and their small-world network properties of clustering and short paths have been exploited computationally to produce biologically relevant information, they have not been truly explored as such, i.e. as navigable small-world networks in the original spirit of Milgram's work. This research seeks to fill this gap by exploring local search on a network representation of proteins and to probe the source of navigability in proteins. Previously, we confirmed that proteins are navigable small-world networks and observed that local search paths exhibit different characteristics from global search paths. In this paper, we investigate the biological relevance of the differences in path characteristics on a type III receptor tyrosine kinase (KIT).
Edit intent: coherence
Original:  Findings from this comparison suggest that EDS paths are more plausible discrete models of intra-protein communication pathways than BFS paths, or at least EDS pathscan provide different insights not readily available with BFS paths.
Revised:  A chief difference that works in favour of local search paths as intra-protein communication pathways than BFS paths, or at least EDS pathscan provide different insights not readily available with BFS paths.
Edit intent: clarity
Original: The Kirchhoff-law-Johnson-(like)-noise (KLJN) is an unconditionally secure key exchange system based on the laws of classical statistical physics.
Revised: The Kirchhoff-law-Johnson-(like)-noise (KLJN) is a secure key exchange system based on the laws of classical statistical physics.
Edit intent: clarity
Original:  Simulation results show that privacy amplification can efficiently mitigate the leak while a capacitor killer can fully eliminate it .
Revised:  Simulation results show that privacy amplification and/or capacitor killer (capacitance compensation) arrangements can effectively eliminate the leak .
Edit intent: clarity
Original: The  Kirchhoff-law-Johnson-(like)-noise (KLJN) is a secure key exchange system  based on the laws of classical statistical physics.
Revised: The security of the Kirchhoff-law-Johnson-(like)-noise (KLJN) is a secure key exchange system based on the laws of classical statistical physics.
Edit intent: clarity
Original: The  Kirchhoff-law-Johnson-(like)-noise (KLJN) is a secure key exchange system  based on the laws of classical statistical physics.
Revised: The Kirchhoff-law-Johnson-(like)-noise (KLJN) key exchange system based on the laws of classical statistical physics.
Edit intent: clarity
Original: The  Kirchhoff-law-Johnson-(like)-noise (KLJN) is a secure key exchange system  based on the laws of classical statistical physics.
Revised: The Kirchhoff-law-Johnson-(like)-noise (KLJN) is a secure key exchange system is based on the laws of classical statistical physics.
Edit intent: fluency
Original:  Similarly to quantum key distribution, in practical situations, due to the non-idealities of the building elements, there is a small information leak, which can be mitigated by privacy amplification or other technique so that the unconditional (information theoretic) security is preserved.
Revised:  Similarly to quantum key distribution, in practical situations, due to the non-idealities of the building elements, there is a small information leak, which can be mitigated by privacy amplification or other techniques so that the unconditional (information theoretic) security is preserved.
Edit intent: fluency
Original:  The control methods of this paper were applied to a mutated cell-cycle model and to a p53-mdm2 model to identify potential control targets.
Revised:  The control methods of this paper were applied to a mutated cell-cycle model and to a p53-mdm2 model to identify potential control targets.
Edit intent: fluency
Original:  As a result , many large-scale data processing environments include collaborative filtering models for which the Alternating Least Squares (ALS) algorithm is used to compute latent factor matrix decompositions.
Revised:  For example , many large-scale data processing environments include collaborative filtering models for which the Alternating Least Squares (ALS) algorithm is used to compute latent factor matrix decompositions.
Edit intent: coherence
Original:  In this paper, we significantly accelerate the convergence of parallel ALS-based optimization methods for collaborative filtering using a nonlinear conjugate gradient (NCG) wrapper around the ALS iterations.
Revised:  In this paper, we propose an approach to accelerate the convergence of parallel ALS-based optimization methods for collaborative filtering using a nonlinear conjugate gradient (NCG) wrapper around the ALS iterations.
Edit intent: clarity
Original:  We also provide a parallel implementation of the accelerated ALS-NCG algorithm in the distributed Apache Spark data processing environment  and an efficient line search technique requiring only 1 map-reduce operation on distributed datasets.
Revised:  We also provide a parallel implementation of the accelerated ALS-NCG algorithm in the Apache Spark distributed data processing environment and an efficient line search technique requiring only 1 map-reduce operation on distributed datasets.
Edit intent: fluency
Original:  We also provide a parallel implementation of the accelerated ALS-NCG algorithm in the distributed Apache Spark data processing environment  and an efficient line search technique requiring only 1 map-reduce operation on distributed datasets.
Revised:  We also provide a parallel implementation of the accelerated ALS-NCG algorithm in the distributed Apache Spark data processing environment , and an efficient line search technique requiring only 1 map-reduce operation on distributed datasets.
Edit intent: fluency
Original:  In both serial numerical experiments on a linux workstation and parallel numerical experiments on a 16 node cluster with 256 computing cores,
Revised:  In serial numerical experiments on a linux workstation and parallel numerical experiments on a 16 node cluster with 256 computing cores,
Edit intent: clarity
Original:  we demonstrate using the MovieLens 20M dataset that the combined ALS-NCG method requires many fewer iterations and less time to reach high ranking accuracies than standalone ALS  . In parallel, NCG-ALS achieves an acceleration factor of 4 or greater in clock time when an accurate solution is desired , with the acceleration factor increasing with greater desired accuracy.
Revised:  we demonstrate that the combined ALS-NCG method requires many fewer iterations and less time to reach high ranking accuracies than standalone ALS . In parallel, NCG-ALS achieves an acceleration factor of 4 or greater in clock time when an accurate solution is desired , with the acceleration factor increasing with greater desired accuracy.
Edit intent: coherence
Original:  we demonstrate using the MovieLens 20M dataset that the combined ALS-NCG method requires many fewer iterations and less time to reach high ranking accuracies than standalone ALS  . In parallel, NCG-ALS achieves an acceleration factor of 4 or greater in clock time when an accurate solution is desired , with the acceleration factor increasing with greater desired accuracy.
Revised:  we demonstrate using the MovieLens 20M dataset that the combined ALS-NCG method requires many fewer iterations and less time than standalone ALS . In parallel, NCG-ALS achieves an acceleration factor of 4 or greater in clock time when an accurate solution is desired , with the acceleration factor increasing with greater desired accuracy.
Edit intent: clarity
Original:  we demonstrate using the MovieLens 20M dataset that the combined ALS-NCG method requires many fewer iterations and less time to reach high ranking accuracies than standalone ALS  . In parallel, NCG-ALS achieves an acceleration factor of 4 or greater in clock time when an accurate solution is desired , with the acceleration factor increasing with greater desired accuracy.
Revised:  we demonstrate using the MovieLens 20M dataset that the combined ALS-NCG method requires many fewer iterations and less time to reach high ranking accuracies than standalone ALS . In parallel, ALS-NCG can achieve an acceleration factor of 4 or greater in clock time when an accurate solution is desired , with the acceleration factor increasing with greater desired accuracy.
Edit intent: clarity
Original:  we demonstrate using the MovieLens 20M dataset that the combined ALS-NCG method requires many fewer iterations and less time to reach high ranking accuracies than standalone ALS  . In parallel, NCG-ALS achieves an acceleration factor of 4 or greater in clock time when an accurate solution is desired , with the acceleration factor increasing with greater desired accuracy.
Revised:  we demonstrate using the MovieLens 20M dataset that the combined ALS-NCG method requires many fewer iterations and less time to reach high ranking accuracies than standalone ALS . In parallel, NCG-ALS achieves an acceleration factor of 4 or greater in clock time when an accurate solution is desired ; furthermore, the acceleration factor increasing with greater desired accuracy.
Edit intent: coherence
Original:  Furthermore , the NCG acceleration mechanism is fully parallelizable and scales linearly with problem size on  datasets with up to nearly 1 billion ratings.
Revised:  Furthermore , the NCG acceleration mechanism is efficient in parallel and scales linearly with problem size on datasets with up to nearly 1 billion ratings.
Edit intent: clarity
Original:  Our NCG acceleration approach is versatile and may be used to accelerate other parallel optimization methods such as stochastic gradient descent and coordinate descent .
Revised:  The acceleration mechanism is general and may also be applicable to other optimization methods for collaborative filtering .
Edit intent: clarity
Original:  It has been furthermore believed by many that the relative phase deviations would prevent the relative phase Toffolis from being very helpful in practical large-scale designs.
Revised:  It was commonly believed that the relative phase deviations would prevent the relative phase Toffolis from being very helpful in practical large-scale designs.
Edit intent: clarity
Original:  In this paper, we report three circuit identities that provide the means for replacing  multiple control Toffoli gates with their simpler relative phase implementations, up to a selectable unitary on certain qubits, and without changing the overall functionality.
Revised:  In this paper, we report three circuit identities that provide the means for replacing certain configurations of the multiple control Toffoli gates with their simpler relative phase implementations, up to a selectable unitary on certain qubits, and without changing the overall functionality.
Edit intent: clarity
Original:  In the present paper we  employ the theoretical tools developed in network theory , in order to shed light on the response of world wide trade to the financial crisis of 2007.
Revised:  In the present paper we employ the theoretical tools of network theory to shed light on the response of world wide trade to the financial crisis of 2007.
Edit intent: clarity
Original:  In the present paper we  employ the theoretical tools developed in network theory , in order to shed light on the response of world wide trade to the financial crisis of 2007.
Revised:  In the present paper we employ the theoretical tools developed in network theory , in order to shed light on the response of world trade to the financial crisis of 2007.
Edit intent: fluency
Original:  In other words, as 2007 approaches the World Trade Web becomes more and more compatible with the picture of a bipartite network where correlations between countries and products are progressively lost.
Revised:  In other words, as 2007 approaches the World Trade Web becomes more and more compatible with the picture of a network where correlations between countries and products are progressively lost.
Edit intent: clarity
Original:  Moreover, the trends characterizing the z-scores of the considered family of motifs suggest that the most evident modification in the structure of the world trade network can be considered as concluded in 2010, after a seemingly stationary phase of three years.
Revised:  Moreover, the most evident modification in the structure of the world trade network can be considered as concluded in 2010, after a seemingly stationary phase of three years.
Edit intent: coherence