wanyu/IteraTeR_v2 huggingface dataset:
Original:  Systems biology aims at distilling these interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding of how higher level functions emerge from the combined action of many biomolecules.
Revised:  Theoretical biology aims at distilling these interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding of how higher level functions emerge from the combined action of many biomolecules.
Edit intent: clarity
Original:  Thus, in this work, we present a computational framework for handling the parameters of the cell models and the optical physics governing bioimaging systems , and for generating the digital images of the cell simulation results after accounting for the systematic effects.
Revised:  Thus, in this work, we present a computational framework for handling the parameters of the cell models and the optical physics governing bioimaging systems . Simulation using this framework allows for generating the digital images of the cell simulation results after accounting for the systematic effects.
Edit intent: clarity
Original:  Simulation using this framework allows for generating the digital images of the cell simulation results after accounting for the systematic effects.
Revised:  Simulation using this framework can generate the digital images of the cell simulation results after accounting for the systematic effects.
Edit intent: clarity
Original: Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomenon in biological cells.
Revised: Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells.
Edit intent: fluency
Original:  Theoretical biology aims at distilling these interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding of how higher level functions emerge from the combined action of many biomolecules.
Revised:  Theoretical biology aims at distilling those interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding of how higher level functions emerge from the combined action of many biomolecules.
Edit intent: fluency
Original:  Theoretical biology aims at distilling these interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding of how higher level functions emerge from the combined action of many biomolecules.
Revised:  Theoretical biology aims at distilling these interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding how higher level functions emerge from the combined action of many biomolecules.
Edit intent: fluency
Original:  Theoretical biology aims at distilling these interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding of how higher level functions emerge from the combined action of many biomolecules.
Revised:  Theoretical biology aims at distilling these interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding of how higher level functions emerge from the combined action of biomolecules.
Edit intent: clarity
Original:  However, there still remain great challenges in bridging the gaps between bioimaging and mathematical modeling.
Revised:  However, there still remain formidable challenges in bridging the gaps between bioimaging and mathematical modeling.
Edit intent: clarity
Original:  However, there still remain great challenges in bridging the gaps between bioimaging and mathematical modeling.
Revised:  However, there still remain great challenges in bridging the gap between bioimaging and mathematical modeling.
Edit intent: coherence
Original:  Generally, the measurements using such fluorescence microscopy systems are influenced by the systematic effects that arise from the stochastic nature of biological cells, the imaging apparatus, and optical physics.
Revised:  Generally, measurements using fluorescence microscopy systems are influenced by the systematic effects that arise from the stochastic nature of biological cells, the imaging apparatus, and optical physics.
Edit intent: clarity
Original:  Generally, the measurements using such fluorescence microscopy systems are influenced by the systematic effects that arise from the stochastic nature of biological cells, the imaging apparatus, and optical physics.
Revised:  Generally, the measurements using such fluorescence microscopy systems are influenced by systematic effects that arise from the stochastic nature of biological cells, the imaging apparatus, and optical physics.
Edit intent: fluency
Original:  Generally, the measurements using such fluorescence microscopy systems are influenced by the systematic effects that arise from the stochastic nature of biological cells, the imaging apparatus, and optical physics.
Revised:  Generally, the measurements using such fluorescence microscopy systems are influenced by the systematic effects that arise from stochastic nature of biological cells, the imaging apparatus, and optical physics.
Edit intent: fluency
Original:  Such systematic effects are always present in all bioimaging systems and hinder the quantitative comparison between the cell model and bioimages.
Revised:  Such systematic effects are always present in all bioimaging systems and hinder quantitative comparison between the cell model and bioimages.
Edit intent: fluency
Original:  Computational tools for such comparisons are still missing .
Revised:  Computational tools for such a comparison are still unavailable .
Edit intent: clarity
Original:  Bioimaging simulation modules using this framework can generate the digital images of the cell simulation results after accounting for the systematic effects.
Revised:  Simulation using this framework can generate the digital images of the cell simulation results after accounting for the systematic effects.
Edit intent: clarity
Original:  Bioimaging simulation modules using this framework can generate the digital images of the cell simulation results after accounting for the systematic effects.
Revised:  Bioimaging simulation modules using this framework can generate digital images of the cell simulation results after accounting for the systematic effects.
Edit intent: fluency
Original:  Bioimaging simulation modules using this framework can generate the digital images of the cell simulation results after accounting for the systematic effects.
Revised:  Bioimaging simulation modules using this framework can generate the digital images of cell simulation results after accounting for the systematic effects.
Edit intent: fluency
Original:  We then demonstrate that such a framework allows the comparison at the level of photon-counting units.
Revised:  We then demonstrate that such a framework enables comparison at the level of photon-counting units.
Edit intent: fluency
Original:  We consider such an approach which uses single locus variants: pairs of isolates whose DNA differ at a single gene locus.
Revised:  We consider such an approach which uses single-locus variants: pairs of isolates whose DNA differ at a single gene locus.
Edit intent: fluency
Original:  Both our test and method for constructing confidence intervals are obtained by modelling the dependence structure in the data, and then applying asymptotic theory regarding the distribution of estimators obtained using a composite likelihood.
Revised:  Both our test and method for constructing confidence intervals are obtained by modeling the dependence structure in the data, and then applying asymptotic theory regarding the distribution of estimators obtained using a composite likelihood.
Edit intent: fluency
Original: In the last few years, the study of multi-layer complex networks has received significant attention.
Revised: In recent years, the study of multi-layer complex networks has received significant attention.
Edit intent: clarity
Original: In the last few years, the study of multi-layer complex networks has received significant attention.
Revised: In the last few years, the study of multi-layer networks has received significant attention.
Edit intent: clarity
Original:  In this work , we provide new measures to analyse dependencies between directed links in different layers of multiplex networks.
Revised:  In this work , we provide new measures of dependency between directed links in different layers of multiplex networks.
Edit intent: clarity
Original:  In this work , we provide new measures to analyse dependencies between directed links in different layers of multiplex networks.
Revised:  In this work , we provide new measures to analyse dependencies between directed links across different layers of multiplex networks.
Edit intent: clarity
Original:  We show that this  requires more than a straightforward extension of the corresponding multiplexity measures that have been developed for undirected multiplexes.
Revised:  We show that this operation requires more than a straightforward extension of the corresponding multiplexity measures that have been developed for undirected multiplexes.
Edit intent: clarity
Original:  Here we extend this quantity to directed multiplexes and introduce the notion of multireciprocity, defined as the tendency of links in one layer to be reciprocated by links in a different layer.
Revised:  Here we extend this quantity to multiplexes and introduce the notion of multireciprocity, defined as the tendency of links in one layer to be reciprocated by links in a different layer.
Edit intent: clarity
Original:   We introduce multireciprocity measures valid for both binary and weighted networks and then validate these novel quantities on the World Trade Multiplex (WTM), representing the import-export bilateral relations between world countries in different commodities .
Revised:  We introduce multireciprocity metrics valid for both binary and weighted networks and then validate these novel quantities on the World Trade Multiplex (WTM), representing the import-export bilateral relations between world countries in different commodities .
Edit intent: clarity
Original:   We introduce multireciprocity measures valid for both binary and weighted networks and then validate these novel quantities on the World Trade Multiplex (WTM), representing the import-export bilateral relations between world countries in different commodities .
Revised:  We introduce multireciprocity measures valid for both binary and weighted networks and then measure these quantities on the World Trade Multiplex (WTM), representing the import-export bilateral relations between world countries in different commodities .
Edit intent: clarity
Original:   We introduce multireciprocity measures valid for both binary and weighted networks and then validate these novel quantities on the World Trade Multiplex (WTM), representing the import-export bilateral relations between world countries in different commodities .
Revised:  We introduce multireciprocity measures valid for both binary and weighted networks and then validate these novel quantities on the World Trade Multiplex (WTM), representing the import-export relationships between world countries in different commodities .
Edit intent: clarity
Original:   We introduce multireciprocity measures valid for both binary and weighted networks and then validate these novel quantities on the World Trade Multiplex (WTM), representing the import-export bilateral relations between world countries in different commodities .
Revised:  We introduce multireciprocity measures valid for both binary and weighted networks and then validate these novel quantities on the World Trade Multiplex (WTM), representing the import-export bilateral relations between world countries in different products .
Edit intent: clarity
Original:  Moreover, we find that most of the pairs of commodities are characterised by positive multireciprocities, even though such values are significantly lower than the usual reciprocity measured on the aggregated network.
Revised:  Moreover, we find that most pairs of commodities are characterised by positive multireciprocities, even though such values are significantly lower than the usual reciprocity measured on the aggregated network.
Edit intent: clarity
Original:  Moreover, we find that most of the pairs of commodities are characterised by positive multireciprocities, even though such values are significantly lower than the usual reciprocity measured on the aggregated network.
Revised:  Moreover, we find that most of the pairs of commodities are characterised by positive multireciprocity, and that such values are significantly lower than the usual reciprocity measured on the aggregated network.
Edit intent: coherence
Original: In recent years, the study of multi-layer networks has received much attention.
Revised: In multi-layer networks has received much attention.
Edit intent: clarity
Original:  We show that this operation requires more than a straightforward extension of the corresponding multiplexity measures that have been developed for undirected multiplexes.
Revised:  We show that this operation requires more than a straightforward extension of the multiplexity measures that have been developed for undirected multiplexes.
Edit intent: clarity
Original:  We introduce multireciprocity metrics valid for both binary and weighted networks and then measure these quantities on the World Trade Multiplex (WTM), representing the import-export relationships between world countries in different products.
Revised:  We introduce multireciprocity metrics valid for both binary and weighted multiplexes and provide an empirical analysis of the World Trade Multiplex (WTM), representing the import-export relationships between world countries in different products.
Edit intent: clarity
Original:  We show that several pairs of layers exhibit strong multiplexity, an effect which can however be largely encoded into the degree or strength sequences of individual layers.
Revised:  We show that several pairs of layers exhibit strong multiplexity, an effect which is however largely encoded into the degree or strength sequences of individual layers.
Edit intent: coherence
Original:   We finally identify robust empirical patterns that allow us to use the multireciprocity matrix to retrieve the two-layer reciprocated degree (strength) of a node from the ordinary in-degree (in-strength) in a single layer and to reconstruct joint multi-layer connection probabilities  from marginal ones , hence bridging the gap between single-layer properties and truly multiplex information.
Revised:  We finally identify robust empirical patterns showing that joint multi-layer connection probabilities from marginal ones , hence bridging the gap between single-layer properties and truly multiplex information.
Edit intent: clarity
Original:   We finally identify robust empirical patterns that allow us to use the multireciprocity matrix to retrieve the two-layer reciprocated degree (strength) of a node from the ordinary in-degree (in-strength) in a single layer and to reconstruct joint multi-layer connection probabilities  from marginal ones , hence bridging the gap between single-layer properties and truly multiplex information.
Revised:  We finally identify robust empirical patterns that allow us to use the multireciprocity matrix to retrieve the two-layer reciprocated degree (strength) of a node from the ordinary in-degree (in-strength) in a single layer and to reconstruct joint multi-layer connection probabilities can be reconstructed from marginal ones , hence bridging the gap between single-layer properties and truly multiplex information.
Edit intent: clarity
Original:   We finally identify robust empirical patterns that allow us to use the multireciprocity matrix to retrieve the two-layer reciprocated degree (strength) of a node from the ordinary in-degree (in-strength) in a single layer and to reconstruct joint multi-layer connection probabilities  from marginal ones , hence bridging the gap between single-layer properties and truly multiplex information.
Revised:  We finally identify robust empirical patterns that allow us to use the multireciprocity matrix to retrieve the two-layer reciprocated degree (strength) of a node from the ordinary in-degree (in-strength) in a single layer and to reconstruct joint multi-layer connection probabilities from marginal ones via the multireciprocity matrix. Therefore the latter can bridge the gap between single-layer properties and truly multiplex information.
Edit intent: clarity
Original: In multi-layer networks with directed links , introducing measures of dependency between different layersrequires more than a straightforward extension of the multiplexity measures that have been developed for undirected multiplexes.
Revised: Real-world multi-layer networks with directed links , introducing measures of dependency between different layersrequires more than a straightforward extension of the multiplexity measures that have been developed for undirected multiplexes.
Edit intent: clarity
Original:  Here we extend it to multiplexes and introduce the notion of multireciprocity, defined as the tendency of links in one layer to be reciprocated by  links in a different layer.
Revised:  Here we extend it to multiplexes and introduce the notion of multireciprocity, defined as the tendency of links in one layer can be reciprocated by links in a different layer.
Edit intent: clarity
Original:  While ordinary reciprocity reduces to a scalar quantity, multireciprocity requires a square matrix generated by all the possible pairs of layers.
Revised:  Multireciprocity generalizes the scalar definition of single-layer reciprocity to that of a square matrix involving all pairs of layers.
Edit intent: clarity
Original:  We introduce multireciprocity metrics valid for both binary and weighted multiplexes and provide an empirical analysis of the World Trade Multiplex (WTM), representing the import-export relationships between world countries in different products .
Revised:  We introduce multiplexity and multireciprocity matrices for both binary and weighted multiplexes and provide an empirical analysis of the World Trade Multiplex (WTM), representing the import-export relationships between world countries in different products .
Edit intent: clarity
Original:  We introduce multireciprocity metrics valid for both binary and weighted multiplexes and provide an empirical analysis of the World Trade Multiplex (WTM), representing the import-export relationships between world countries in different products .
Revised:  We introduce multireciprocity metrics valid for both binary and weighted multiplexes and provide an empirical analysis of the World Trade Multiplex (WTM), representing the import-export relationships between world countries in different commodities .
Edit intent: clarity
Original:  We also find that most pairs of commodities are characterised by positive multireciprocity, andthat such values are significantly lower than the usual reciprocity measured on the aggregated network.
Revised:  We also find that most pairs of commodities are characterised by positive multireciprocity, andthat such values are significantly lower than the usual reciprocity measured on the aggregate network.
Edit intent: fluency
Original:  Moreover, layers with low (high) internal reciprocity are embedded within groups of layers with  low (high) mutual multireciprocity.
Revised:  Moreover, layers with low (high) internal reciprocity are embedded within sets of layers with low (high) mutual multireciprocity.
Edit intent: clarity
Original:  We validated the library by solving three different multiscale problems which also served to demonstrate the flexibility of the framework in handling heterogeneous models and solvers.
Revised:  We validated the library by solving three different multiscale problems , which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers.
Edit intent: fluency
Original:  In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the the effect of surface grafting on the hydrodynamics properties on the surface.
Revised:  In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface.
Edit intent: fluency
Original:  We also investigate the effect of airway constriction and tissue weakening on the ventilation, tissue stress and alveolar pressure distribution and highlight the interdependence of ventilation and deformation  .
Revised:  We also investigate the effect of airway constriction and tissue weakening on the ventilation, tissue stress and alveolar pressure distribution . The key advantage of the model is the ability to provide insight into the mutual dependence between ventilation and deformation .
Edit intent: clarity
Original:  We also investigate the effect of airway constriction and tissue weakening on the ventilation, tissue stress and alveolar pressure distribution and highlight the interdependence of ventilation and deformation  .
Revised:  We also investigate the effect of airway constriction and tissue weakening on the ventilation, tissue stress and alveolar pressure distribution and highlight the interdependence of ventilation and deformation . This is essential when studying lung diseases, such as chronic obstructive pulmonary disease and pulmonary fibrosis. Thus the model can be used to form a better understanding of integrated lung mechanics in both the healthy and diseased states .
Edit intent: coherence
Original:  Among other things, we show that TD methods can identify structures that correlate strongly with the core-periphery structure of realistic networks, even when using simple greedy heuristics;
Revised:  Our main contributions are the following: we show that TD methods can identify structures that correlate strongly with the core-periphery structure of realistic networks, even when using simple greedy heuristics;
Edit intent: clarity
Original:  Our  detailed empirical results for different TD heuristics on toy and synthetic networks help to establish a baseline to understand better the behavior of the heuristics on more complex real-world networks;
Revised:  Our detailed empirical results for TD heuristics on toy and synthetic networks help to establish a baseline to understand better the behavior of the heuristics on more complex real-world networks;
Edit intent: clarity
Original:  Our  detailed empirical results for different TD heuristics on toy and synthetic networks help to establish a baseline to understand better the behavior of the heuristics on more complex real-world networks;
Revised:  Our detailed empirical results for different TD heuristics on toy and synthetic networks to establish a baseline to understand better the behavior of the heuristics on more complex real-world networks;
Edit intent: coherence
Original:  and our results here suggest future directions for the development of improved TD heuristics that are more appropriate for improved structure identification in realistic networks .
Revised:  and our results here suggest future directions for improved TD heuristics that are more appropriate for improved structure identification in realistic networks .
Edit intent: clarity
Original:  and our results here suggest future directions for the development of improved TD heuristics that are more appropriate for improved structure identification in realistic networks .
Revised:  and our results here suggest future directions for the development of improved TD heuristics that are more appropriate for realistic social graphs .
Edit intent: clarity
Original: We model the ligand-receptor molecular communication channel with a discrete-time Markov model, and show how to obtain the capacity of this channel  .
Revised: We model biochemical signal transduction, based on a ligand-receptor molecular communication channel with a discrete-time Markov model, and show how to obtain the capacity of this channel .
Edit intent: clarity