wanyu/IteraTeR_v2 huggingface dataset:
Original:  We observe evidence of widespread selection on the D. simulans X, suggesting adaptation through duplication is common on the X.
Revised:  We document evidence of widespread selection on the D. simulans X, suggesting adaptation through duplication is common on the X.
Edit intent: clarity
Original:  Whole gene duplication rates are low at 1.1 \times 10^{-9\times10 in D. yakuba and 6.1 \times 10\times10 ^{ -9 }  in D. simulans, suggesting long wait times for new mutations  .
Revised:  Whole gene duplication rates are low at 1.1 \times 10^{-9\times10 in D. yakuba and 6.1 \times 10\times10 ^{ -10 } in D. simulans, suggesting long wait times for new mutations .
Edit intent: fluency
Original:  Hence, parallel recruitment of the same duplicated gene in different species will be rare and standing variation will define evolutionary outcomes , in spite of convergence across  rapidly evolving phenotypes.
Revised:  Hence, parallel recruitment of the same duplicated gene in different species will be rare and standing variation will define evolutionary outcomes in spite of convergence across rapidly evolving phenotypes.
Edit intent: fluency
Original: We study the computational complexity of the recently proposed nubots model of molecular-scale self-assembly.
Revised: We study the computational complexity of the recently proposed nubot model of molecular-scale self-assembly.
Edit intent: fluency
Original:  The model generalises asynchronous cellular automaton to have non-local movement where large assemblies of molecules can be moved around, analogous to millions of molecular motors in animal muscle effecting the rapid movement of macroscale arms and legs.
Revised:  The model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be moved around, analogous to millions of molecular motors in animal muscle effecting the rapid movement of macroscale arms and legs.
Edit intent: fluency
Original:  We show that nubots is capable of simulating Boolean circuits of polylogarithmic depth and polynomial size, in only polylogarithmic expected time.
Revised:  We show that the nubot model is capable of simulating Boolean circuits of polylogarithmic depth and polynomial size, in only polylogarithmic expected time.
Edit intent: clarity
Original:  In computational complexity terms, we show that any problem from the complexity class NC is solved in polylogarithmic expected time on nubots that use a polynomial amount of workspace .
Revised:  In computational complexity terms, we show that any problem from the complexity class NC is solvable in polylogarithmic expected time on nubots that use a polynomial amount of workspace .
Edit intent: clarity
Original:  In computational complexity terms, we show that any problem from the complexity class NC is solved in polylogarithmic expected time on nubots that use a polynomial amount of workspace .
Revised:  In computational complexity terms, we show that any problem from the complexity class NC is solved in polylogarithmic expected time and polynomial workspace using nubots .
Edit intent: clarity
Original:  Circuit depth is a well-studied notion of parallel time, and our result implies that nubots is a highly parallel model of computation in a formal sense.
Revised:  Circuit depth is a well-studied notion of parallel time, and our result implies that the nubot model is a highly parallel model of computation in a formal sense.
Edit intent: clarity
Original:  Asynchronous cellular automata are not capable of such parallelism, and our result shows that adding a  movement primitive to such a model, to get the nubots model, drastically increases parallel processing abilities.
Revised:  Asynchronous cellular automata are not capable of this parallelism, and our result shows that adding a movement primitive to such a model, to get the nubots model, drastically increases parallel processing abilities.
Edit intent: fluency
Original:  Asynchronous cellular automata are not capable of such parallelism, and our result shows that adding a  movement primitive to such a model, to get the nubots model, drastically increases parallel processing abilities.
Revised:  Asynchronous cellular automata are not capable of such parallelism, and our result shows that adding a movement primitive to such a model, to get the nubot model, drastically increases parallel processing abilities.
Edit intent: fluency
Original:  We highlight conceptual and mathematical inconsistencies throughout the development of decision theory, whose correction clarifies that the modern perspective is legitimate and that boundedness of utility functionsis not required .
Revised:  We highlight conceptual and mathematical inconsistencies throughout the development of decision theory, whose correction clarifies that our perspective is legitimate and that boundedness of utility functionsis not required .
Edit intent: clarity
Original:  We prove that for any set of fixed constraints, such graphs are "multipodal": asymptotically in the number of vertices there is a partition of the vertices into M < \infty subsets V_1, V_2, \ldots, V_M, and a set of well-defined probabilities q _{ij} of an edge between any v_i \in V_i and v_j \in V_j.
Revised:  We prove that under such constraints graphs are "multipodal": asymptotically in the number of vertices there is a partition of the vertices into M < \infty subsets V_1, V_2, \ldots, V_M, and a set of well-defined probabilities q _{ij} of an edge between any v_i \in V_i and v_j \in V_j.
Edit intent: clarity
Original:  Finally, we give evidence based on simulation, that throughout the space of the constraint parameters of the 2-star model the graphs are not just multipodal but bipodal (M= 2 ), easily understood as extensions of the known optimizers \le \le   on the boundary of the parameter space , and that the degenerate optima correspond to a non-analyticity in the entropy .
Revised:  Finally, we give evidence based on simulation, that throughout the space of the constraint parameters of the 2-star model the graphs are not just multipodal but bipodal (M= 2 \le \le on the boundary of the parameter space , and that the degenerate optima correspond to a non-analyticity in the entropy .
Edit intent: clarity
Original:  While there is a simple combinatorial \frac{1 algorithm, the best hardness result remains at \frac{1 assuming the Unique Games Conjecture (UGC). -rounds of the Sherali-Adams hierarchy of linear programming for Graph Pricing is at most 1/2 + \epsilon.
Revised:  While there is a simple combinatorial \frac{1 algorithm, the best hardness result remains at 1/2 assuming the Unique Games Conjecture (UGC). -rounds of the Sherali-Adams hierarchy of linear programming for Graph Pricing is at most 1/2 + \epsilon.
Edit intent: fluency
Original:  }  Besides its connection to Graph Pricing, the hardness of Generalized Max-Dicut is interesting in its own right since in most 2-ary CSPs studied in the literature, SDP-based algorithms perform better than LP-based or combinatorial algorithms --- for this 2-ary CSP, a simple combinatorial algorithm does the best.
Revised:  } Besides its connection to Graph Pricing, the hardness of Generalized Max-Dicut is interesting in its own right since in most arity two CSPs studied in the literature, SDP-based algorithms perform better than LP-based or combinatorial algorithms --- for this 2-ary CSP, a simple combinatorial algorithm does the best.
Edit intent: clarity
Original:  }  Besides its connection to Graph Pricing, the hardness of Generalized Max-Dicut is interesting in its own right since in most 2-ary CSPs studied in the literature, SDP-based algorithms perform better than LP-based or combinatorial algorithms --- for this 2-ary CSP, a simple combinatorial algorithm does the best.
Revised:  } Besides its connection to Graph Pricing, the hardness of Generalized Max-Dicut is interesting in its own right since in most 2-ary CSPs studied in the literature, SDP-based algorithms perform better than LP-based or combinatorial algorithms --- for this arity two CSP, a simple combinatorial algorithm does the best.
Edit intent: clarity
Original: Multilayer relationships among  and information about biological entities must be accompanied by the means to analyze, visualize, and obtain insights from such data.
Revised: Multilayer relationships among entities and information about biological entities must be accompanied by the means to analyze, visualize, and obtain insights from such data.
Edit intent: clarity
Original: Multilayer relationships among  and information about biological entities must be accompanied by the means to analyze, visualize, and obtain insights from such data.
Revised: Multilayer relationships among and information about entities must be accompanied by the means to analyze, visualize, and obtain insights from such data.
Edit intent: clarity
Original: Given two point sets in the plane, we study the minimization of the (lexicographic) bottleneck distance between the smaller set and an equally sized subset of the larger set under translations.
Revised: Given two point sets in the plane, we study the minimization of the bottleneck distance between the smaller set and an equally sized subset of the larger set under translations.
Edit intent: clarity
Original:  We relate this problem to two Voronoi-type diagrams and derive polynomial bounds for their combinatorial complexity that are optimal in the size of the larger set .
Revised:  We relate this problem to two Voronoi-type diagram and derive polynomial bounds for their combinatorial complexity that are optimal in the size of the larger set .
Edit intent: fluency
Original:  We relate this problem to two Voronoi-type diagrams and derive polynomial bounds for their combinatorial complexity that are optimal in the size of the larger set .
Revised:  We relate this problem to two Voronoi-type diagrams and derive polynomial bounds for its complexity that are optimal in the size of the larger set .
Edit intent: clarity
Original:  We relate this problem to two Voronoi-type diagrams and derive polynomial bounds for their combinatorial complexity that are optimal in the size of the larger set .
Revised:  We relate this problem to two Voronoi-type diagrams and derive polynomial bounds for their combinatorial complexity that are optimal in the size of A .
Edit intent: clarity
Original:  Our analysis reveals remarkable predictability for long-prevailing scientific concepts based on the levels of their prior usage.
Revised:  Our analysis reveals great predictability for long-prevailing scientific concepts based on the levels of their prior usage.
Edit intent: clarity
Original: High-throughput experiments in bacteria and eukaryotic cells have identified tens of thousands of possible interactions between proteins.
Revised: High-throughput experiments in bacteria and eukaryotic cells have identified tens of thousands of interactions between proteins.
Edit intent: clarity
Original:  Here we present a new generalized method showing that patterns of evolutionary sequence changes across proteins reflect residues that are close in space, and with sufficient accuracy to determine the three-dimensional structure of the protein complexes.
Revised:  Here we present a new generalized method showing that patterns of evolutionary sequence changes across proteins reflect residues that are close in space, with sufficient accuracy to determine the three-dimensional structure of the protein complexes.
Edit intent: coherence
Original:  We demonstrate that the inferred evolutionary coupling scores  distinguish between interacting and non-interacting proteins and the accurate prediction of residue interactions .
Revised:  We demonstrate that the inferred evolutionary coupling scores distinguish between interacting and non-interacting proteins .
Edit intent: clarity
Original: High-throughput experiments in bacteria and eukaryotic cells have identified tens of thousands of interactions between proteins.
Revised: Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions between proteins.
Edit intent: clarity
Original:  Here we present a new generalized method showing that patterns of evolutionary sequence changes across proteins reflect residues that are close in space , with sufficient accuracy to determine the three-dimensional structure of the protein complexes.
Revised:  Here we present a new generalized method showing that patterns of evolutionary sequence changes across proteins identifies residues that are close in space , with sufficient accuracy to determine the three-dimensional structure of the protein complexes.
Edit intent: clarity
Original:  Here we present a new generalized method showing that patterns of evolutionary sequence changes across proteins reflect residues that are close in space , with sufficient accuracy to determine the three-dimensional structure of the protein complexes.
Revised:  Here we present a new generalized method showing that patterns of evolutionary sequence changes across proteins reflect residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes.
Edit intent: fluency
Original:  We also show how to build networks having given density distributions, which gives us further insight into the structure of real networks.
Edit intent: coherence
Original: The different cell types in a living organism are an outcome of the process of cell differentiation in which a progenitor cell state differentiates into two distinct cell types.
Revised: The different cell types in a living organism acquire their identity through the process of cell differentiation in which a progenitor cell state differentiates into two distinct cell types.
Edit intent: clarity
Original: The different cell types in a living organism are an outcome of the process of cell differentiation in which a progenitor cell state differentiates into two distinct cell types.
Revised: The different cell types in a living organism are an outcome of the process of cell differentiation in which the multipotent progenitor cells differentiate into distinct cell types.
Edit intent: clarity
Original:  Experimental evidence and analysis of large-scale microarray data establish the key role of a two-gene motif in the process of cell differentiation .
Revised:  Experimental evidence and analysis of large-scale microarray data establish the key role played by a two-gene motif in the process of cell differentiation .
Edit intent: clarity
Original:  Experimental evidence and analysis of large-scale microarray data establish the key role of a two-gene motif in the process of cell differentiation .
Revised:  Experimental evidence and analysis of large-scale microarray data establish the key role of a two-gene motif in cell differentiation in a number of cell systems .
Edit intent: clarity
Original:  A number of theoretical models have recently been proposed based on the two-gene motif to provide a physical understanding of how cell differentiation works .
Revised:  A number of theoretical models have recently been proposed based on the two-gene motif to provide a physical understanding of how cell differentiation occurs .
Edit intent: clarity
Original:  The latter repress each other's activity directly through DNA binding and indirectly through the formation of heterodimers.
Revised:  The later repress each other's activity directly through DNA binding and indirectly through the formation of heterodimers.
Edit intent: fluency
Original:  The deterministic dynamics of our model give rise to a supercritical pichfork bifurcation from an undifferentiated stable steady state to two differentiated stable steady states.
Revised:  The deterministic dynamics of our model give rise to a supercritical pitchfork bifurcation from an undifferentiated stable steady state to two differentiated stable steady states.
Edit intent: fluency
Original:  The stochastic dynamics of our model are studied using the approach based on the Langevin equations  .
Revised:  The stochastic dynamics of our model are studied using the approaches based on the Langevin equations .
Edit intent: fluency
Original:  The simulation results are consistent with the recent experimental observations.
Revised:  The simulation results provide a new physical understanding of recent experimental observations.
Edit intent: clarity
Original:  The later repress each other's activity directly through DNA binding and indirectly through the formation of heterodimers.
Revised:  The latter repress each other's activity directly through DNA binding and indirectly through the formation of heterodimers.
Edit intent: fluency
Original:  We also give (1-\varepsilon)-approximation algorithms that take time O(\varepsilon^{-3/2}+ \varepsilon^{-1/2} \log n) for maximizing the area and O(\varepsilon^{-3+ \varepsilon^{-1} \log n) for maximizing the perimeter} .
Revised:  We also give (1-\varepsilon)-approximation algorithms that take time O(\varepsilon^{-3/2}+ \varepsilon^{-1/2} \log n) + \varepsilon^{-1} \log n) for maximizing the perimeter} .
Edit intent: clarity
Original: The fitness of somatic cells of metazoan, the ability of proliferation and survival, depends greatly on the level of microenvironment.
Revised: The fitness of somatic cells of metazoan, the ability of proliferation and survival, depends on microenvironment.
Edit intent: clarity
Original:  In somatic evolution, a mutated cell in a tissue clonally expands abnormally because of a high fitness as normal cells and a corresponding microenvironment.
Revised:  In somatic evolution, a mutated cell in a tissue clonally expands abnormally because of its high fitness as normal cells and a corresponding microenvironment.
Edit intent: clarity
Original:  In somatic evolution, a mutated cell in a tissue clonally expands abnormally because of a high fitness as normal cells and a corresponding microenvironment.
Revised:  In somatic evolution, a mutated cell in a tissue clonally expands abnormally because of a high fitness as normal cells in a corresponding microenvironment.
Edit intent: clarity
Original:  In this study, we propose the cancer cell hypothesis (CCH) that cancer cells are the mutated cells with two characteristics: clonal expansion and actively damaging the microenvironment by some behaviors, such as producing more poison in metabolism than normal cells.
Revised:  In this study, we propose the cancer cell hypothesis that cancer cells are the mutated cells with two characteristics: clonal expansion and actively damaging the microenvironment by some behaviors, such as producing more poison in metabolism than normal cells.
Edit intent: clarity
Original:  In this study, we propose the cancer cell hypothesis (CCH) that cancer cells are the mutated cells with two characteristics: clonal expansion and actively damaging the microenvironment by some behaviors, such as producing more poison in metabolism than normal cells.
Revised:  In this study, we propose the cancer cell hypothesis (CCH) that cancer cells are the mutated cells with two characteristics: clonal expansion and damaging the microenvironment by some behaviors, such as producing more poison in metabolism than normal cells.
Edit intent: clarity
Original:  In this study, we propose the cancer cell hypothesis (CCH) that cancer cells are the mutated cells with two characteristics: clonal expansion and actively damaging the microenvironment by some behaviors, such as producing more poison in metabolism than normal cells.
Revised:  In this study, we propose the cancer cell hypothesis (CCH) that cancer cells are the mutated cells with two characteristics: clonal expansion and actively damaging the microenvironment through the behaviours such as producing more poison in metabolism than normal cells.
Edit intent: clarity
Original:  CCH gives a rational explanation for cancer invasion and metastasis, which are still controversial in mechanism .
Revised:  This model provides an explanation for the nature of invasion and metastasis, which are still controversial in mechanism .
Edit intent: clarity
Original:  CCH gives a rational explanation for cancer invasion and metastasis, which are still controversial in mechanism .
Revised:  CCH gives a rational explanation for cancer invasion and metastasis, which are still controversial .
Edit intent: clarity
Original:  In addition, we theoretically reasoned out that normal cells have almost the highest fitness in healthy microenvironment as a result of long-term organic evolution.
Revised:  In addition, we theoretically reasoned out that normal cells have almost the highest fitness in healthy microenvironments as a result of long-term organic evolution.
Edit intent: fluency
Original:  This conclusion inspires a general therapy of cancer, improving microenvironment which relies on a mechanism differing from chemotherapy and targeted therapy.
Revised:  This inspires a new kind of therapy of cancer, improving microenvironment which relies on a mechanism differing from chemotherapy and targeted therapy.
Edit intent: clarity
Original: We introduce a family of  norms \| \cdot \|_{1,2,s} on R^n and define a distribution over random matrices \Phi_s \in R^{m \times n} parametrized by sparsity level s such that for a fixed set X of n points in R^n, we have for m \geq C s \log( n) that with high probability, 1{2} \| x \|_{1,2,s} \leq \| \Phi_s (x) \|_1 \leq 2 \| x\|_{1,2,s} for all x\in X. Several existing results in the literature reduce to special cases of this result at different values of s:
Revised: For a family of norms \| \cdot \|_{1,2,s} on R^n and define a distribution over random matrices \Phi_s \in R^{m \times n} parametrized by sparsity level s such that for a fixed set X of n points in R^n, we have for m \geq C s \log( n) that with high probability, 1{2} \| x \|_{1,2,s} \leq \| \Phi_s (x) \|_1 \leq 2 \| x\|_{1,2,s} for all x\in X. Several existing results in the literature reduce to special cases of this result at different values of s:
Edit intent: coherence
Original: We introduce a family of  norms \| \cdot \|_{1,2,s} on R^n and define a distribution over random matrices \Phi_s \in R^{m \times n} parametrized by sparsity level s such that for a fixed set X of n points in R^n, we have for m \geq C s \log( n) that with high probability, 1{2} \| x \|_{1,2,s} \leq \| \Phi_s (x) \|_1 \leq 2 \| x\|_{1,2,s} for all x\in X. Several existing results in the literature reduce to special cases of this result at different values of s:
Revised: We introduce a family of norms \| \cdot \|_{1,2,s} on R^n , we provide a distribution over random matrices \Phi_s \in R^{m \times n} parametrized by sparsity level s such that for a fixed set X of n points in R^n, we have for m \geq C s \log( n) that with high probability, 1{2} \| x \|_{1,2,s} \leq \| \Phi_s (x) \|_1 \leq 2 \| x\|_{1,2,s} for all x\in X. Several existing results in the literature reduce to special cases of this result at different values of s:
Edit intent: clarity
Original: We introduce a family of  norms \| \cdot \|_{1,2,s} on R^n and define a distribution over random matrices \Phi_s \in R^{m \times n} parametrized by sparsity level s such that for a fixed set X of n points in R^n, we have for m \geq C s \log( n) that with high probability, 1{2} \| x \|_{1,2,s} \leq \| \Phi_s (x) \|_1 \leq 2 \| x\|_{1,2,s} for all x\in X. Several existing results in the literature reduce to special cases of this result at different values of s:
Revised: We introduce a family of norms \| \cdot \|_{1,2,s} on R^n and define a distribution over random matrices \Phi_s \in R^{m \times n} parametrized by sparsity level s such that for a fixed set X of K points in R^n, we have for m \geq C s \log( n) that with high probability, 1{2} \| x \|_{1,2,s} \leq \| \Phi_s (x) \|_1 \leq 2 \| x\|_{1,2,s} for all x\in X. Several existing results in the literature reduce to special cases of this result at different values of s:
Edit intent: clarity