wanyu/IteraTeR_v2 huggingface dataset:
Original: We consider the variant of monotone simultaneous embeddings of directed graphs where all graphs are directed paths and directions of monotonicity are different .
Revised: We consider the variant of monotone simultaneous embeddings of upward planar digraphs, which are simultaneous embeddings where the drawing of each digraph is upward planar, and the directions of the upwardness of different graphs can differ. We first consider the special case where each digraph is a directed path.
Edit intent: clarity
Original:  In contrast to the known result that any two directed paths admit a monotone simultaneous embedding, we show that there exist examples of three paths that do not admit such an embedding for any possible choice of directions of monotonicity.
Revised:  In contrast to the known result that any two directed paths admit a monotone simultaneous embedding, there exist examples of three paths that do not admit such an embedding for any possible choice of directions of monotonicity.
Edit intent: coherence
Original: Finally, we provide a polynomial-time algorithm that, given any number of paths and predefined directions of monotonicity, decides whether  a monotone simultaneous embedding with respect to the given directions exists .
Revised: Finally, we provide a polynomial-time algorithm that, given any number of paths and predefined directions of monotonicity, decides whether the paths admit a monotone simultaneous embedding with respect to the given directions exists .
Edit intent: clarity
Original:  We extend previous multi-agent-based, spatial models of democracy by adding a new class of agents, oligarchs , which represent leaders of firms in a common industry who lobby for beneficial subsidies through campaign donations  .
Revised:  We extend the existing literature on agent-based models of political economy in the following manner: (1) by introducing a new class of agents, oligarchs , which represent leaders of firms in a common industry who lobby for beneficial subsidies through campaign donations .
Edit intent: clarity
Original:  We extend previous multi-agent-based, spatial models of democracy by adding a new class of agents, oligarchs , which represent leaders of firms in a common industry who lobby for beneficial subsidies through campaign donations  .
Revised:  We extend previous multi-agent-based, spatial models of democracy by adding a new class of agents- oligarchs - that represent leaders of firms in a common industry who lobby for beneficial subsidies through campaign donations .
Edit intent: coherence
Original:  By verifying that central hypotheses from the economics literature hold for the OLIGO model, we accomplish two goals: (1) We show that the simple rules agents follow in our model are sufficient to capture much of the complex dynamics of this politico-economic system;
Revised:  Our key results indicate that (1) We show that the simple rules agents follow in our model are sufficient to capture much of the complex dynamics of this politico-economic system;
Edit intent: clarity
Original: Time-frequency representations (TFRs) of signals, such as  windowed Fourier transform (WFT), wavelet transform (WT) and their synchrosqueezed variants (SWFT, SWT), provide powerful analysis tools.
Revised: Time-frequency representations (TFRs) of signals, such as the windowed Fourier transform (WFT), wavelet transform (WT) and their synchrosqueezed variants (SWFT, SWT), provide powerful analysis tools.
Edit intent: fluency
Original: The hydration thermodynamics of the GXG tripeptide relative to the reference GGG defines theconditional hydration contribution of X.
Revised: The hydration thermodynamics of the GXG tripeptide relative to the reference GGG conditional hydration contribution of X.
Edit intent: clarity
Original: The extraction of oscillatory components and their properties from different time-frequency representations, such as windowed Fourier transform , wavelet transformor their synchrosqueezed versions , is an important topic in signal processing.
Revised: The extraction of oscillatory components and their properties from different time-frequency representations, such as windowed Fourier transform and wavelet transform , is an important topic in signal processing.
Edit intent: clarity
Original:  This is not a trivial issue, and the best procedure for extraction is still not settled or agreed.
Revised:  This is not a trivial issue, and the optimal method for extraction is still not settled or agreed.
Edit intent: clarity
Original:  We discuss and develop the procedures that can be used for this task and compare their performance, based on both simulated and real data.
Revised:  We discuss and develop procedures that can be used for this task and compare their performance, based on both simulated and real data.
Edit intent: fluency
Original:  The first step in this procedure is to extract the ridge curve: a sequence of amplitude peak positions (ridge points), corresponding to the component of interest.
Revised:  The first step in this procedure is to find an appropriate ridge curve: a sequence of amplitude peak positions (ridge points), corresponding to the component of interest.
Edit intent: clarity
Original:  We discuss and develop procedures that can be used for this task and compare their performance , based on both simulated and real data.
Revised:  We discuss and develop procedures that can be used for this task and compare their performance on both simulated and real data.
Edit intent: coherence
Original:  Additionally , we propose a fast algorithm for optimization of a path functional of particular form over all possible ridge sequences.
Revised:  In particular , we propose a fast algorithm for optimization of a path functional of particular form over all possible ridge sequences.
Edit intent: coherence
Original: Persistence homology is a vital tool for topological data analysis.
Revised: Persistent homology is a vital tool for topological data analysis.
Edit intent: fluency
Original:  Previous work has devel- oped some statistical estimators for characteristics of collections of persistence diagrams.
Revised:  Previous work has developed some statistical estimators for characteristics of collections of persistence diagrams.
Edit intent: fluency
Original:  However, tools that provide statistical inference for scenarios in which the observations are persistence diagrams are not developed.
Revised:  However, tools that provide statistical inference for observations that are persistence diagrams are not developed.
Edit intent: clarity
Original: Directional cell migrationis a process involved in many physiological phenomena being mainly associated to chemical cues in vivo.
Revised: Many physiological phenomena involve directional cell migration. It is usually attributed to chemical gradients in vivo.
Edit intent: clarity
Original:  Recently, in vitro cell guiding assays have been realized by means of stiffness/adhesion gradients or micro-patterned adhesive motifs.
Revised:  Recently, other cues have been shown to guide cells in vitro, including stiffness/adhesion gradients or micro-patterned adhesive motifs.
Edit intent: clarity
Original:  The cellular mechanisms leading to biased migration remain however widely unknownand often even the direction of motion is unpredictable.
Revised:  However, the cellular mechanism leading to these biased migrations remains unknown, and, often, even the direction of motion is unpredictable.
Edit intent: clarity
Original:  We identified the concept of efficient protrusion and  associated direction index.
Revised:  We identified the concept of efficient protrusion and an associated direction index.
Edit intent: fluency
Original:  Our analysis of protrusion statistics enabled the quantitative prediction of cell trajectories in situations where we varied external cues (adhesive patterns) and internal cues (protrusion activity), and strikingly even made possible to sustainably drive cell motion in the direction opposite to that predicted by their imposed polarization.
Revised:  Our analysis of the protrusion statistics facilitated the quantitative prediction of cell trajectories in situations where we varied external cues (adhesive patterns) and internal cues (protrusion activity), and strikingly even made possible to sustainably drive cell motion in the direction opposite to that predicted by their imposed polarization.
Edit intent: clarity
Original:  Based on only two measured cellular parameters at short timescales, we developed a theoretical model showing that asymmetry of protrusion activity and their stabilization are sufficient for predicting all measures associated with  long-term motion .
Revised:  Based on only two measured cellular parameters at short timescales, we developed a theoretical model showing that an asymmetry in the protrusion fluctuations is sufficient for predicting all measures associated with long-term motion .
Edit intent: clarity
Original:  Based on only two measured cellular parameters at short timescales, we developed a theoretical model showing that asymmetry of protrusion activity and their stabilization are sufficient for predicting all measures associated with  long-term motion .
Revised:  Based on only two measured cellular parameters at short timescales, we developed a theoretical model showing that asymmetry of protrusion activity and their stabilization are sufficient for predicting all measures associated with the long-term motion .
Edit intent: fluency
Original:  We formulate the inference of condition specific network structures that incorporates relevant prior knowledge as a convex optimization problem, and develop an efficient learning algorithm to jointly infer the biological networks as well as their changes.
Revised:  We formulate the inference of condition specific network structures that incorporates relevant prior knowledge as a convex optimization problem, and developed an efficient learning algorithm to jointly infer the biological networks as well as their changes.
Edit intent: fluency
Original:  We then apply our method to yeast cell line data and breast cancer microarray data and obtain biologically plausible results.
Revised:  We then applied our method to yeast cell line data and breast cancer microarray data and obtain biologically plausible results.
Edit intent: fluency
Original:  We then apply our method to yeast cell line data and breast cancer microarray data and obtain biologically plausible results.
Revised:  We then apply our method to yeast cell line and breast cancer microarray data and obtain biologically plausible results.
Edit intent: fluency
Original:  We then apply our method to yeast cell line data and breast cancer microarray data and obtain biologically plausible results.
Revised:  We then apply our method to yeast cell line data and breast cancer microarray data and obtained biologically plausible results.
Edit intent: fluency
Original:  We prove that the intersection graphs of simple families of compact arc-connected sets in the plane pierced by a common line have chromatic number bounded by a function of their clique number.
Revised:  It is proved that the intersection graphs of simple families of compact arc-connected sets in the plane pierced by a common line have chromatic number bounded by a function of their clique number.
Edit intent: clarity
Original: We discuss the measures hd(F) ( "hardness" ) and whd(F) ("w-hardness") in relation to resolutionand space complexity bounds;
Revised: Various "hardness" ) and whd(F) ("w-hardness") in relation to resolutionand space complexity bounds;
Edit intent: clarity
Original: Intratumor heterogeneity is both a major confounding factor in studying individual clones and an information source in characterizing tumor system.
Revised: Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing tumor system.
Edit intent: clarity
Original:  Systematic efforts to characterize intratumor genomic heterogeneity must effectively distinguish significant genuine clonal sequences from probabilistic fake derivatives.
Revised:  Systematic efforts to characterize intercellular genomic heterogeneity must effectively distinguish significant genuine clonal sequences from probabilistic fake derivatives.
Edit intent: clarity
Original:  Systematic efforts to characterize intratumor genomic heterogeneity must effectively distinguish significant genuine clonal sequences from probabilistic fake derivatives.
Revised:  Systematic efforts to characterize intratumor genomic heterogeneity must effectively distinguish genuine clonal sequences from probabilistic fake derivatives.
Edit intent: clarity
Original:  Systematic efforts to characterize intratumor genomic heterogeneity must effectively distinguish significant genuine clonal sequences from probabilistic fake derivatives.
Revised:  Systematic efforts to characterize intratumor genomic heterogeneity must effectively distinguish significant genuine clonal sequences from fake derivatives.
Edit intent: clarity
Original:  We developed a software tool (SIGH) for identifying significant intratumor genomic heterogeneity directly from mixed sequencing reads that can improve genomic analyses in many oncological contexts.
Revised:  We developed a novel approach (SIGH) for identifying significant intratumor genomic heterogeneity directly from mixed sequencing reads that can improve genomic analyses in many oncological contexts.
Edit intent: clarity
Original:  We developed a software tool (SIGH) for identifying significant intratumor genomic heterogeneity directly from mixed sequencing reads that can improve genomic analyses in many oncological contexts.
Revised:  We developed a software tool (SIGH) for identifying significant intratumor genomic heterogeneity directly from mixed sequencing reads that can improve genomic analyses in many biological contexts.
Edit intent: clarity
Original:  This open source software offers several attractive features: (1) it is supported by a well-grounded statistical framework that exploits probabilistic characteristics of sequencing errors;
Revised:  This method offers several attractive features: (1) it is supported by a well-grounded statistical framework that exploits probabilistic characteristics of sequencing errors;
Edit intent: clarity
Original:  This open source software offers several attractive features: (1) it is supported by a well-grounded statistical framework that exploits probabilistic characteristics of sequencing errors;
Revised:  This open source software offers several attractive features: (1) it is supported by a well grounded statistical framework that exploits probabilistic characteristics of sequencing errors;
Edit intent: fluency
Original:  SIGH also provides the users with the ability to utilize parallel computing on ubiquitous multicore machines .
Revised:  Extensive realistic simulation studies show that our method can reliably estimate the error rates and faithfully distinguish the genuine clones from fake derivatives, paving the way for follow up analysis that is otherwise ruined by the often dominant fake clones .
Edit intent: coherence
Original: Estimating the number of triangles in a graph given as a stream of edges is a fundamental problem in data mining.
Revised: Real-world graphs often manifest as a massive temporal stream of edges is a fundamental problem in data mining.
Edit intent: clarity
Original: Self-sustainability for energy scavenging networks is a crucial step in modern sensor network developments.
Revised: Self-sustainability is a crucial step in modern sensor network developments.
Edit intent: clarity
Original:  Here, we offer a comprehensive framework for self-sufficient sensor networks powered by renewable energy sources.
Revised:  Here, we offer a comprehensive framework for autonomous sensor networks powered by renewable energy sources.
Edit intent: clarity
Original:  Our framework   permits to gauge the impact of key sensor network parameters, such as the battery size , the harvester size (e.g., solar panel), the information transmission rate and the nodes' duty cycle.
Revised:  Our framework permits to gauge the impact of key sensor network parameters, such as the battery size , the harvester size , the information transmission rate and the nodes' duty cycle.
Edit intent: coherence
Original:  Our framework   permits to gauge the impact of key sensor network parameters, such as the battery size , the harvester size (e.g., solar panel), the information transmission rate and the nodes' duty cycle.
Revised:  Our framework permits to gauge the impact of key sensor network parameters, such as the battery size , the harvester size (e.g., solar panel), the information transmission rate and the radio duty cycle.
Edit intent: clarity
Original:  Finally, we provide results describing the consequences of most of the relevant design choices in terms of network behavior, maximum achievable throughput and dynamics associated with the optimal energy management policies .
Revised:  Finally, we provide results describing the consequences of most of the relevant design choices in terms of achievable network throughput and battery level dynamics .
Edit intent: clarity
Original: Language universals have been longly attributed to an innate Universal Grammar.
Revised: Language universals have long been attributed to an innate Universal Grammar.
Edit intent: fluency
Original:  An alternative explanation states that linguistic universals emerged independently in every language in response to shared cognitive , though non language-specific, biases.
Revised:  An alternative explanation states that linguistic universals emerged independently in every language in response to shared cognitive or perceptual biases.
Edit intent: clarity
Original:  A computational model has recently shown how this could be the case, focusing on the paradigmatic example of the universal properties of color naming patterns, and producing results in accurate agreement with the experimental data.
Revised:  A computational model has recently shown how this could be the case, focusing on the paradigmatic example of the universal properties of colour naming patterns, and producing results in accurate agreement with the experimental data.
Edit intent: fluency
Original:  A computational model has recently shown how this could be the case, focusing on the paradigmatic example of the universal properties of color naming patterns, and producing results in accurate agreement with the experimental data.
Revised:  A computational model has recently shown how this could be the case, focusing on the paradigmatic example of the universal properties of color naming patterns, and producing results in quantitative agreement with the experimental data.
Edit intent: clarity
Original:  Here we investigate thoroughly the role of a cognitive bias in the framework of this model.
Revised:  Here we investigate the role of a cognitive bias in the framework of this model.
Edit intent: clarity
Original:  Here we investigate thoroughly the role of a cognitive bias in the framework of this model.
Revised:  Here we investigate thoroughly the role of a cognitive bias in the framework of the model.
Edit intent: clarity
Original:  We study how, and to what extent, the structure of the bias can influence the corresponding linguistic universal patterns.
Revised:  We study how, and to what extent, the structure of the bias influences the corresponding linguistic universal patterns.
Edit intent: clarity
Original:  We show also that the cultural history of a group of speakers introduces population-specific constraints that act against the uniforming pressure of the cognitive bias, and we clarify the interplay between these two forces .
Revised:  We show that the cultural history of a group of speakers introduces population-specific constraints that act against the uniforming pressure of the cognitive bias, and we clarify the interplay between these two forces .
Edit intent: clarity
Original:  We show also that the cultural history of a group of speakers introduces population-specific constraints that act against the uniforming pressure of the cognitive bias, and we clarify the interplay between these two forces .
Revised:  We show also that the cultural history of a group of speakers introduces population-specific constraints that act against the pressure for uniformity arising from the individual bias, and we clarify the interplay between these two forces .
Edit intent: clarity
Original:  While the vast majority of theoretical studies neglects detritus, from our results it follows that the detrital food web is more stable than its grazing counterpart, because the interactions mediated by detritus dump out fluctuations in species' densities.
Revised:  While the vast majority of theoretical studies neglects detritus, from our results it follows that the detrital food web is more stable than its grazing counterpart, because the interactions mediated by detritus damp out fluctuations in species' densities.
Edit intent: clarity
Original:  We present formulas for elementary collisions tests with these orbit shapes and we suggest an algorithm, based on motion subdivision and computation of bounding balls, that can give a no-collision guarantee.
Revised:  We present formulas for elementary collision tests with these orbit shapes and we suggest an algorithm, based on motion subdivision and computation of bounding balls, that can give a no-collision guarantee.
Edit intent: fluency
Original: Citation networks form directed acyclic graphs .
Revised: In many complex networks the vertices are ordered in time, and edges represent causal connections. We propose methods of analysing such directed acyclic graphs .
Edit intent: clarity
Original: Cell functional diversity is a major but poorly-understood influence of biological processes . Most accounts of diversity involve a search for sequence or expression differences.
Revised: Cell functional diversity is a significant determinant on how biological processes unfold . Most accounts of diversity involve a search for sequence or expression differences.
Edit intent: clarity
Original:  The reconstruction of gene regulatory networks from observational data is a challenging task, especially , considering the large number of involved players (e.g. genes) and much fewer biological replicates available for analysis.
Revised:  The reconstruction of gene regulatory networks from observational data is a challenging task, especially considering the large number of involved players (e.g. genes) and much fewer biological replicates available for analysis.
Edit intent: fluency
Original:  The reconstruction of gene regulatory networks from observational data is a challenging task, especially , considering the large number of involved players (e.g. genes) and much fewer biological replicates available for analysis.
Revised:  The reconstruction of gene regulatory networks from observational data is a challenging task, especially , considering the large number of players (e.g. genes) and much fewer biological replicates available for analysis.
Edit intent: clarity
Original:  The reconstruction of gene regulatory networks from observational data is a challenging task, especially , considering the large number of involved players (e.g. genes) and much fewer biological replicates available for analysis.
Revised:  The reconstruction of gene regulatory networks from observational data is a challenging task, especially , considering the large number of involved players (e.g. genes) involved and the small number of biological replicates available for analysis.
Edit intent: clarity
Original:  Herein, we proposed a new statistical method of estimating the number of erroneous edges  that strongly enhances the commonly used inference approaches.
Revised:  Herein, we propose a new statistical method of estimating the number of erroneous edges that strongly enhances the commonly used inference approaches.
Edit intent: fluency