wanyu/IteraTeR_v2 huggingface dataset:
Original:  Finally, we prove that if f is a conjunctive network then every subnetwork of f (and f itself in particular) has at most one fixed point if and only if f has no subnetworks in%DIFDELCMD < \C%%% ^+.
Revised:  Finally, we prove that if f is a conjunctive network then every subnetwork of f (and f itself in particular) has at most one fixed point if and only if f has no %DIFDELCMD < \C%%% ^+.
Edit intent: clarity
Original: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene transfers, gene duplication and subsequent neofunctionalization) will cause some genes to exhibit a history quite distinct from the histories of the majority of genes.
Revised: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene transfers, gene duplication and subsequent neofunctionalization) will cause some genes to exhibit a history quite distinct from those of the majority of genes.
Edit intent: clarity
Original:  In contrast to parametric models, such as  coalescent, nonparametric approaches avoid the problem of model mis-specification, which leads to potentially unreliable results.
Revised:  In contrast to parametric models, such as the coalescent, nonparametric approaches avoid the problem of model mis-specification, which leads to potentially unreliable results.
Edit intent: fluency
Original:  Our method demonstrated superior accuracyin outlier detection on simulated data, when compared to a previously published method.
Revised:  Our method demonstrated superior accuracyin outlier detection on simulated data, when compared to a recently published method.
Edit intent: clarity
Original:  We also applied our method to a dataset of Apicomplexa genes, identifying a set of putative outliers .
Revised:  We also applied our method to a data set of Apicomplexa genes, identifying a set of putative outliers .
Edit intent: fluency
Original:  We also applied our method to a dataset of Apicomplexa genes, identifying a set of putative outliers .
Revised:  We also applied our method to a dataset of Apicomplexa genes, as well as a set of putative outliers .
Edit intent: clarity
Original:  In this paper we propose and implement , kdetrees, a nonparametric method of estimating distributions of phylogenetic trees, with the goal of identifying trees which are significantly different from the rest of the trees in the sample.
Revised:  Results: We propose and implement , kdetrees, a nonparametric method of estimating distributions of phylogenetic trees, with the goal of identifying trees which are significantly different from the rest of the trees in the sample.
Edit intent: coherence
Original:  In this paper we propose and implement , kdetrees, a nonparametric method of estimating distributions of phylogenetic trees, with the goal of identifying trees which are significantly different from the rest of the trees in the sample.
Revised:  In this paper we propose and implement KDETREES, a nonparametric method of estimating distributions of phylogenetic trees, with the goal of identifying trees which are significantly different from the rest of the trees in the sample.
Edit intent: fluency
Original:  In the case of the Apicomlexa, kdetrees identified several unreliable sequences which had escaped previous detection, as well as gene indepentenly reported as a probably case of horizontal gene transfer.
Revised:  In the case of the Apicomlexa, kdetrees identified several unreliable sequences which had escaped previous detection, as well as a gene independently reported as a probably case of horizontal gene transfer.
Edit intent: fluency
Original:  In the case of the Apicomlexa, kdetrees identified several unreliable sequences which had escaped previous detection, as well as gene indepentenly reported as a probably case of horizontal gene transfer.
Revised:  In the case of the Apicomlexa, kdetrees identified several unreliable sequences which had escaped previous detection, as well as gene indepentenly reported as a possible case of horizontal gene transfer.
Edit intent: clarity
Original:  Moreover, we show that computing the VC-dimension is NP-complete and that it remains NP-complete for planar graphs in the case k =  2. This is done by a reduction from a variant of Planar 1-In-3-Sat which we prove to be NP-complete .
Revised:  Moreover, we show that computing the VC-dimension is NP-complete and that it remains NP-complete for planar graphs in the cases k = 2. This is done by a reduction from a variant of Planar 1-In-3-Sat which we prove to be NP-complete .
Edit intent: fluency
Original:  In classic work, Fisher and Muller proposed that recombination provides an evolutionary advantage in large populations by alleviating this competition.
Revised:  Fisher and Muller proposed that recombination provides an evolutionary advantage in large populations by alleviating this competition.
Edit intent: clarity
Original:  Based on recent progress in quantifying the speed of adaptation in asexual populations undergoing clonal interference, we present a detailed analysis of the Fisher-Muller mechanism for a model genome consisting of two loci with an infinite number of beneficial alleles each and multiplicative (non-epistatic) fitness effects.
Revised:  Based on recent progress in quantifying the speed of adaptation in asexual populations undergoing clonal interference, we present a detailed analysis of the Fisher-Muller mechanism for a model genome consisting of two loci with an infinite number of beneficial alleles each and multiplicative fitness effects.
Edit intent: clarity
Original:  We solve the deterministic, infinite population dynamics exactly and show that, for a particular, natural mutation scheme, the speed of adaptation in sexuals is twice as large as in asexuals.
Revised:  We solve the infinite population dynamics exactly and show that, for a particular, natural mutation scheme, the speed of adaptation in sexuals is twice as large as in asexuals.
Edit intent: clarity
Original:  This result is argued to hold for any nonzero value of the rate of recombination.
Edit intent: clarity
Original:  The simulations also show that recombination leads to a strong equalization of the number of fixed mutations in the  two loci  .
Revised:  The simulations also show that the two loci .
Edit intent: clarity
Original:  For a particular communal recombination scheme , the ratio of the sexual to asexual adaptation speed is approximately equal to L in large populations  .
Revised:  If each offspring samples the alleles at each locus from the gene pool of the whole population rather than from two parents , the ratio of the sexual to asexual adaptation speed is approximately equal to L in large populations .
Edit intent: clarity
Original:  Rather than simply correlating one-dimensional local volatility models for each asset, our approach could be dubbed a multidimensional local volatility approach with state dependent diffusion matrix.
Revised:  Our approach could be dubbed a multidimensional local volatility approach with state dependent diffusion matrix.
Edit intent: clarity
Original:  A comparison with the standard approach consisting in using Monte Carlo simulation that samples simply-correlated suitably discretized one-dimensional  paths is made .
Revised:  A comparison with sampling simply-correlated suitably discretized one-dimensional paths is made .
Edit intent: clarity
Original:  The previously published co-crystal structure implies two important hydrogen bonding networks in the MACVGP /hTfR1 interface ;
Revised:  The previously published co-crystal structure shows two large hydrogen-bonding networks in the MACVGP /hTfR1 interface ;
Edit intent: clarity
Original:  Finally, we found a viral site known to be critical for infection , may mark an important evolutionary suppressor site for infection-diminishing hTfR1 mutants.
Revised:  Finally, we found a viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-diminishing hTfR1 mutants.
Edit intent: fluency
Original:  Finally, we found a viral site known to be critical for infection , may mark an important evolutionary suppressor site for infection-diminishing hTfR1 mutants.
Revised:  Finally, we found a viral site known to be critical for infection , may mark an important evolutionary suppressor site for infection-resistant hTfR1 mutants.
Edit intent: clarity
Original:  Taken together, our computational data rationalize many of the available experimental data, further refine our biochemical understanding of this system, and point to the most likely next evolutionary step for MACV .
Revised:  Finally, our method provides an elegant framework to compare the effects of multiple mutations, individually and jointly, on protein--protein interactions .
Edit intent: clarity
Original: Existing computational methods to predict protein--protein interaction affinity often perform poorly in important test cases.
Revised: In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein-protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases.
Edit intent: clarity
Original:  We present here a new method to interrogate affinity differences resulting from mutations in a host-virus protein--protein interface.
Revised:  We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host-virus protein--protein interface.
Edit intent: clarity
Original:  We find  that these quantities  provide novel biophysical insight into the GP1/hTfR1 interaction.
Revised:  We find that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction.
Edit intent: clarity
Original:  First, with no prior knowledge of the system we can differentiate among wild-type and mutant complexes.
Revised:  First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes.
Edit intent: fluency
Original:  Finally, our method provides an elegant framework to compare the effects of multiple mutations, individually and jointly, on protein--protein interactions.
Revised:  Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein--protein interactions.
Edit intent: clarity
Original:  Finally, our method provides an elegant framework to compare the effects of multiple mutations, individually and jointly, on protein--protein interactions.
Revised:  Finally, our method provides an elegant framework to compare the effects of multiple mutations, individually and jointly, on protein-protein interactions.
Edit intent: fluency
Original: We study the maximum differential coloring problem, where an n- vertex graph must be labeled with the numbers 1, ..., n such that the minimum difference between the two labels of any edge is maximized.
Revised: We study the maximum differential coloring problem, where the vertices of an n-vertex graph must be labeled with the numbers 1, ..., n such that the minimum difference between the two labels of any edge is maximized.
Edit intent: fluency
Original: We study the maximum differential coloring problem, where an n- vertex graph must be labeled with the numbers 1, ..., n such that the minimum difference between the two labels of any edge is maximized.
Revised: We study the maximum differential coloring problem, where an n- vertex graph must be labeled with the numbers 1, ..., n such that the minimum difference between the two labels of any adjacent vertices is maximized.
Edit intent: clarity
Original:  As it is NP-Hard to find the optimal labels for general graphs, we consider special sub-classes: caterpillars, spiders, and extended stars.
Revised:  As it is NP-hard to find the optimal labels for general graphs, we consider special sub-classes: caterpillars, spiders, and extended stars.
Edit intent: fluency
Original: We study the maximum differential coloring problem , where the vertices of an n-vertex graph must be labeled with the numbers 1 , ..., nsuch that the minimum difference between the two labels of any  adjacent vertices is maximized.
Revised: We study the maximum differential coloring problem , where the vertices of an n-vertex graph must be labeled with the numbers 1 , ..., nsuch that the minimum difference between the two labels of any adjacent vertices is maximized.
Edit intent: fluency
Original: We study the maximum differential coloring problem , where the vertices of an n-vertex graph must be labeled with the numbers 1 , ..., nsuch that the minimum difference between the two labels of any  adjacent vertices is maximized.
Revised: We study the maximum differential coloring problem , where the vertices of an n-vertex graph must be labeled with the numbers 1 to n, so that the minimum difference between the two labels of any adjacent vertices is maximized.
Edit intent: clarity
Original:  As it is NP-hard to find the optimal labels\NPH for general graphs  , we consider special sub-classes: caterpillars, spiders, and extended stars.
Revised:  As the problem is\NPH for general graphs , we consider special sub-classes: caterpillars, spiders, and extended stars.
Edit intent: clarity
Original: Given (planar) graphs G_1=(V,E_1), %DIFDELCMD < \dots%%%  ,G_k=(V,E_k) on n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P\subset\R^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, %DIFDELCMD < \dots%%%  ,G_k under \phi are all plane.
Revised: Given (planar) graphs G_1=(V,E_1), %DIFDELCMD < \dots%%% ... ,G_k=(V,E_k) on n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P\subset\R^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, %DIFDELCMD < \dots%%% ,G_k under \phi are all plane.
Edit intent: fluency
Original: Given (planar) graphs G_1=(V,E_1), %DIFDELCMD < \dots%%%  ,G_k=(V,E_k) on n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P\subset\R^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, %DIFDELCMD < \dots%%%  ,G_k under \phi are all plane.
Revised: Given (planar) graphs G_1=(V,E_1), %DIFDELCMD < \dots%%% ,G_k=(V,E_k) on n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P\subset\R^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, %DIFDELCMD < \dots%%% ,G_k under \phi are all plane.
Edit intent: fluency
Original: Given (planar) graphs G_1=(V,E_1), %DIFDELCMD < \dots%%%  ,G_k=(V,E_k) on n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P\subset\R^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, %DIFDELCMD < \dots%%%  ,G_k under \phi are all plane.
Revised: Given (planar) graphs G_1=(V,E_1), %DIFDELCMD < \dots%%% ,G_k=(V,E_k) on n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P\subset\R^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, %DIFDELCMD < \dots%%% ... ,G_k under \phi are all plane.
Edit intent: coherence
Original: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices,  simultaneous geometric embedding (with mapping)  or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Revised: Given a collection of planar graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Edit intent: clarity
Original: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices,  simultaneous geometric embedding (with mapping)  or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Revised: Given (planar ) graphs G_1 ,\dots n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Edit intent: coherence
Original: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices,  simultaneous geometric embedding (with mapping)  or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Revised: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots,G_k on the same set V of n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Edit intent: clarity
Original: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices,  simultaneous geometric embedding (with mapping)  or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Revised: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices, the simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Edit intent: fluency
Original: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices,  simultaneous geometric embedding (with mapping)  or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Revised: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices, simultaneous geometric embedding (with mapping) problem, or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Edit intent: fluency
Original: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices,  simultaneous geometric embedding (with mapping)  or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, ... \dots ,G_k under \phi are all plane.
Revised: Given (planar ) graphs G_1 =(V,E_1),...,G_k =(V,E_k) on\dots n vertices, simultaneous geometric embedding (with mapping) or simply k-SGE, is the problem of finding a point set P \subset%DIFDELCMD < \R%%% ^2 of size n and a bijection \phi: V \to P such that the induced straight-line drawings of G_1, \dots ,G_k under \phi are all plane.
Edit intent: fluency
Original:  We show that the decision problem k-SGE is complete for%DIFDELCMD < \ER%%%  , the existential theory of the reals.
Revised:  %DIFDELCMD < \ER%%% , the existential theory of the reals.
Edit intent: coherence
Original:  Unlike most existing work our formalism does not rely on a master equation as a starting point , instead it is based on a dynamical generating functional describing the probability measure over all possible paths of the dynamics.
Revised:  Unlike most existing work our formalism does not rely on a master equation , instead it is based on a dynamical generating functional describing the probability measure over all possible paths of the dynamics.
Edit intent: clarity
Original:  Unlike most existing work our formalism does not rely on a master equation as a starting point , instead it is based on a dynamical generating functional describing the probability measure over all possible paths of the dynamics.
Revised:  Unlike most existing work our formalism does not rely on a master equation as a starting point , instead it is based upon a dynamical generating functional describing the probability measure over all possible paths of the dynamics.
Edit intent: fluency
Original:  Exemplars of a model of gene regulation with delayed auto-inhibition and a model of epidemic spread with delayed recovery provide convincing evidence of the applicability of our results.
Revised:  Exemplars of a model of gene regulation with delayed auto-inhibition and a model of epidemic spread with delayed recovery provide evidence of the applicability of our results.
Edit intent: clarity
Original:  In other words, the difference between linearity and negative transitivity is constituted of bubbles .
Revised:  In other words, the difference between linearity and negative transitivity is constituted of balloons .
Edit intent: clarity
Original:  As a consequence of this characterization, under certain natural topological conditions on the preordered set A furnished with its interval topology, the existence of a continuous generalized utility function on A is proved.
Revised:  As a consequence of this characterization, under certain natural topological conditions on the set of preferences A furnished with its interval topology, the existence of a continuous generalized utility function on A is proved.
Edit intent: clarity
Original:  Here, we studied the effect of genetic polymorphisms on transgenerational inheritance of yeast segregants that were derived from a cross between a laboratory strain and a wild strain of Saccharomyces cerevisiae.
Revised:  We studied the effect of genetic polymorphisms on transgenerational inheritance of yeast segregants that were derived from a cross between a laboratory strain and a wild strain of Saccharomyces cerevisiae.
Edit intent: coherence
Original:  We compared segregants with high contents of minor alleles (MAs) of common SNPs relative to those with low contents.
Revised:  We compared segregants with high MA content (MAC) relative to those with low contents.
Edit intent: clarity
Original:  These results suggest a lower capacity to maintain inheritance of traits in individuals or cells with greater genetic variations and have implications for studying common diseases.
Revised:  These results suggest a lower capacity to maintain inheritance of traits in individuals or cells with greater MAC, which have implications for studying common diseases.
Edit intent: clarity
Original:  Finally, using public datasets, we found MAC linkage to mRNA expression of hundreds of genes.
Revised:  Using public datasets, we found MAC linkage to mRNA expression of hundreds of genes.
Edit intent: coherence
Original:  MAC was preferentially linked to traits with high number of known additive QTLs.
Revised:  Finally, we found preferential effect of MAC on traits with high number of known additive QTLs.
Edit intent: clarity
Original: A multiple access relay channel (MARC) is considered in which an (analogue) network coding is implemented in the relay node.
Revised: A multiple access relay channel (MARC) is considered in which an analogue-like network coding is implemented in the relay node.
Edit intent: clarity