wanyu/IteraTeR_v2 huggingface dataset:
Original: Genetic linkage may result in the expression of multiple products from a single polycistronic transcript, under the control of a single promoter.
Revised: Genetic linkage may result in the expression of multiple products from a polycistronic transcript, under the control of a single promoter.
Edit intent: clarity
Original:  However, microRNAs are frequently clustered in the genomes of animals and plants , and these clusters are often transcribed as a single unit.
Revised:  However, microRNAs are frequently clustered in the genomes of animals , and these clusters are often transcribed as a single unit.
Edit intent: clarity
Original:  However, the origin of microRNA clusters has not been so far systematically explored.
Revised:  However, the origin of microRNA clusters has not been so far explored.
Edit intent: clarity
Original:  Here we study the evolution of all microRNA clusters in Drosophila melanogaster , and suggest a number of models for their emergence .
Revised:  Here we study the evolution of microRNA clusters in Drosophila melanogaster , and suggest a number of models for their emergence .
Edit intent: clarity
Original:  Here we study the evolution of all microRNA clusters in Drosophila melanogaster , and suggest a number of models for their emergence .
Revised:  Here we study the evolution of all microRNA clusters in Drosophila melanogaster .
Edit intent: clarity
Original:  We observed that a majority of microRNA clusters arose by the de novo formation of new microRNA-like hairpins in existing microRNA transcripts.
Revised:  We observed that the majority of microRNA clusters arose by the de novo formation of new microRNA-like hairpins in existing microRNA transcripts.
Edit intent: fluency
Original:  Some clusters also emerged by tandem duplication of a single microRNA. Comparative genomics show that these clusters , once formed, are unlikely to split or undergo rearrangements.
Revised:  Some clusters also emerged by tandem duplication of a single microRNA. Comparative genomics show that these clusters are unlikely to split or undergo rearrangements.
Edit intent: clarity
Original:  We propose a model for microRNA cluster origin and evolution in which selection over one of the microRNAs in the cluster interferes with the evolution of the other tightly linked microRNAs.
Revised:  We propose a model for microRNA cluster evolution in which selection over one of the microRNAs in the cluster interferes with the evolution of the other tightly linked microRNAs.
Edit intent: clarity
Original:  We propose a model for microRNA cluster origin and evolution in which selection over one of the microRNAs in the cluster interferes with the evolution of the other tightly linked microRNAs.
Revised:  We propose a model for microRNA cluster origin and evolution in which selection over one of the microRNAs in the cluster interferes with the evolution of the other linked microRNAs.
Edit intent: clarity
Original:  Our analysis suggests that the evolutionary study of microRNAs and other small RNAs must consider and account for linkage associations.
Revised:  Our analysis suggests that the study of microRNAs and other small RNAs must consider and account for linkage associations.
Edit intent: clarity
Original:  Our analysis suggests that the evolutionary study of microRNAs and other small RNAs must consider and account for linkage associations.
Revised:  Our analysis suggests that the evolutionary study of microRNAs and small RNAs must consider and account for linkage associations.
Edit intent: clarity
Original:  Our analysis suggests that the evolutionary study of microRNAs and other small RNAs must consider and account for linkage associations.
Revised:  Our analysis suggests that the evolutionary study of microRNAs and other small RNAs must consider linkage associations.
Edit intent: clarity
Original: Sex in higher diploids carries a two-fold cost of males that should reduce its fitness relative to cloning and result in  extinction.
Revised: Sex in higher diploids carries a two-fold cost of males that should reduce its fitness relative to cloning and result in its extinction.
Edit intent: fluency
Original:  We use computer simulations of finite populations to model a Red Queen in which a parasitic haploid mounts a negative frequency-dependent attack on a diploid host.
Revised:  We use a heuristic approach to model mutation-selection in finite populations where a parasitic haploid mounts a negative frequency-dependent attack on a diploid host.
Edit intent: clarity
Original:  Polyclonal populations disproportionately experience interference with selection at high mutation rates, both between and within loci , slowing clonal population adaptation to a changing parasite environment and reducing clonal population fitness relative to sex.
Revised:  Polyclonal populations disproportionately experience interference with selection at high mutation rates, both between and within loci . This slows clonal population adaptation to a changing parasite environment and reducing clonal population fitness relative to sex.
Edit intent: coherence
Original:  Polyclonal populations disproportionately experience interference with selection at high mutation rates, both between and within loci , slowing clonal population adaptation to a changing parasite environment and reducing clonal population fitness relative to sex.
Revised:  Polyclonal populations disproportionately experience interference with selection at high mutation rates, both between and within loci , slowing clonal population adaptation to a changing parasite environment and reduces clonal population fitness relative to sex.
Edit intent: fluency
Original:  This effect increases markedly with the number of loci under independent selection.
Revised:  The interference increases markedly with the number of loci under independent selection.
Edit intent: clarity
Original: We solve  the optimal trade execution problem in the Almgren and Chirss framework with the Value-at-risk / Expected Shortfall based criterion of Gatheral and Schied when the underlying unaffected stock price follows a displaced diffusion model.
Revised: We solve the optimal trade execution problem when the mid asset price follows a displaced diffusion model.
Edit intent: clarity
Original:  Optimal strategies  under various risk criteria, namely value-at-risk, expected shortfall and a  version of the cost variance measure  are derived and compared.
Revised:  Optimal strategies under various risk criteria, namely value-at-risk, expected shortfall and a version of the cost variance measure , are derived and compared.
Edit intent: fluency
Original:  Optimal solutions across criteria and asset dynamics are comparable although the difference are not negligible for high levels of risk aversion and low market impact assets  .
Revised:  Optimal solutions across criteria and asset dynamics are comparable although differences are not negligible for high levels of risk aversion and low market impact assets .
Edit intent: fluency
Original: We provide a closed form perturbative solution to the M-city network SIS model using the transport rates between cities as a perturbation parameter.
Revised: Herein we provide a closed form perturbative solution to the M-city network SIS model using the transport rates between cities as a perturbation parameter.
Edit intent: clarity
Original: We provide a closed form perturbative solution to the M-city network SIS model using the transport rates between cities as a perturbation parameter.
Revised: We provide a closed form perturbative solution to the M-city network SIS model using the transport rates between nodes as a perturbation parameter.
Edit intent: clarity
Original:  To further corroborate the results, we simulate and analyze a highly infectious SIS outbreak in New Zealand (NZ, Aotearoa) , where we illustrate how the first-order expansion compares to the numerical solution, when we recompose NZ into two subpopulations : Auckland (T\=amaki Makaurau, containing over one third of the total population), and the remainder of NZ.
Revised:  To further corroborate our results, we simulate and analyze a highly infectious SIS outbreak in New Zealand (NZ, Aotearoa) , where we illustrate how the first-order expansion compares to the numerical solution, when we recompose NZ into two subpopulations : Auckland (T\=amaki Makaurau, containing over one third of the total population), and the remainder of NZ.
Edit intent: fluency
Original:  In this comparison we use documented air traffic data, and isolate the country from international travel .
Revised:  In this comparison we use documented air traffic data, and the country is internationally quarantined .
Edit intent: clarity
Original:  We demonstrate that within the first-order solution's range, it compares well to that of the numerical simulations .
Revised:  We demonstrate that our analytical predictions compare well to the numerical solution .
Edit intent: clarity
Original: In social choice settings with linear preferences, random dictatorship is known to be the only social decision scheme satisfying strategyproofness and ex post efficiency 8 . When also allowing indifferences, random serial dictatorship (RSD) is a well-known generalization of random dictatorship that retains both properties.
Revised: In social choice settings with linear preferences, random dictatorship is known to be the only social decision scheme satisfying strategyproofness and ex post efficiency . When also allowing indifferences, random serial dictatorship (RSD) is a well-known generalization of random dictatorship that retains both properties.
Edit intent: coherence
Original: We give a new probabilistic algorithm for interpolating a sparse polynomial f given by a straight-line program.
Revised: We give a new probabilistic algorithm for interpolating a "sparse" polynomial f given by a straight-line program.
Edit intent: fluency
Original:  Our algorithm constructs an approximation f* of f, such that their difference probably has at most half the number of terms of f, then recursively interpolates their difference.
Revised:  Our algorithm constructs an approximation f* of f, such that their difference probably has at most half the number of terms of f, then recurses on their difference.
Edit intent: clarity
Original: The Karoubi envelope of a shift is defined as the Karoubi envelope of the syntactic semigroup of the language of blocks of the shift .
Revised: We prove that the Karoubi envelope of a shift is defined as the Karoubi envelope of the syntactic semigroup of the language of blocks of the shift .
Edit intent: coherence
Original: The Karoubi envelope of a shift is defined as the Karoubi envelope of the syntactic semigroup of the language of blocks of the shift .
Revised: The Karoubi envelope of a shift --- defined as the Karoubi envelope of the syntactic semigroup of the language of blocks of the shift .
Edit intent: clarity
Original:  We prove that , up to natural equivalence of categories, the Karoubi envelope of a shift is invariant under flow equivalence.
Revised:  We prove that , up to natural equivalence of categories, an invariant of flow equivalence.
Edit intent: clarity
Original:   Another application concerns the classification of Markov-Dyck  shifts: it is shown that, under mild conditions, two graphs define flow equivalent Markov-Dyck shifts if and only if they are isomorphic  .
Revised:  Another application concerns the classification of Markov-Dyck shifts: it is shown that, under mild conditions, two graphs define flow equivalent shifts if and only if they are isomorphic .
Edit intent: fluency
Original: The popularization of cloud computing has brought a concern over the energy consumption  in data centers.
Revised: The popularization of cloud computing has raised concerns over the energy consumption in data centers.
Edit intent: clarity
Original: The popularization of cloud computing has brought a concern over the energy consumption  in data centers.
Revised: The popularization of cloud computing has brought a concern over the energy consumption that takes place in data centers.
Edit intent: clarity
Original:  In addition to the energy consumed by servers, the energy consumed by the large number of network devices emerges as a significant problem.
Revised:  In addition to the energy consumed by servers, the energy consumed by large numbers of network devices emerges as a significant problem.
Edit intent: fluency
Original:  Based on this framework, we characterize the problem of achieving energy efficiency with a time-aware model,  prove its NP-hardness and solve it in two steps.
Revised:  Based on this framework, we characterize the problem of achieving energy efficiency with a time-aware model, and we prove its NP-hardness and solve it in two steps.
Edit intent: coherence
Original:  Based on this framework, we characterize the problem of achieving energy efficiency with a time-aware model,  prove its NP-hardness and solve it in two steps.
Revised:  Based on this framework, we characterize the problem of achieving energy efficiency with a time-aware model, prove its NP-hardness with a solution that has two steps.
Edit intent: clarity
Original:  First, we solve the problem of assigning virtual machines (VM) to servers to reduce the amount of traffic and to generate favorable conditions for energy-efficient routing .
Revised:  First, we solve the problem of assigning virtual machines (VM) to servers to reduce the amount of traffic and to generate favorable conditions for traffic engineering .
Edit intent: clarity
Original:  The solution proposed for this problem is based on three essential principles  we propose.
Revised:  The solution reached for this problem is based on three essential principles we propose.
Edit intent: clarity
Original:  The solution proposed for this problem is based on three essential principles  we propose.
Revised:  The solution proposed for this problem is based on three essential principles that we propose.
Edit intent: clarity
Original:  Experimental results show that, by using the whole framework, we can achieve up to 50 \% energy savings.
Revised:  Experimental results confirm that, by using the whole framework, we can achieve up to 50 \% energy savings.
Edit intent: clarity
Original:  Experimental results show that, by using the whole framework, we can achieve up to 50 \% energy savings.
Revised:  Experimental results show that, by using this framework, we can achieve up to 50 \% energy savings.
Edit intent: clarity
Original:  Experimental results show that, by using the whole framework, we can achieve up to 50 \% energy savings.
Revised:  Experimental results show that, by using the whole framework, we can achieve up to 50 percent energy savings.
Edit intent: fluency
Original:  Extensions to general cases prove that our method is scalable and practical in use .
Revised:  We also provide a comprehensive discussion on the scalability and practicability of the framework .
Edit intent: clarity
Original: Tip-driven growth processes underlie the development of many complex biological organisms .
Revised: Tip-driven growth processes underlie the development of many plants .
Edit intent: clarity
Original:  To date, tip-driven growth processes have been modeled as an elongating path or series of segments without taking into account lateral expansion during elongation.
Revised:  To date, tip-driven growth processes have been modelled as an elongating path or series of segments without taking into account lateral expansion during elongation.
Edit intent: fluency
Original:  Modeling expansion in this way can lead to contradictions in the physical plausibility of the resulting surface and to uncertainty about how the object reached certain regions of space.
Revised:  Modelling expansion in this way can lead to contradictions in the physical plausibility of the resulting surface and to uncertainty about how the object reached certain regions of space.
Edit intent: clarity
Original:  In 2D, the fiber walk takes place on a square lattice and the space occupied by the fiber is modeled as a lateral contraction of the lattice.
Revised:  In 2D, the fiber walk takes place on a square lattice and the space occupied by the fiber is modelled as a lateral contraction of the lattice.
Edit intent: fluency
Original:  We show that fiber walks generate a fiber that have well-defined curvatures, enable the identification of the process underlying the occupancy of physical space.
Revised:  We show that fiber walks generate fibers that have well-defined curvatures, enable the identification of the process underlying the occupancy of physical space.
Edit intent: fluency
Original:  Hence, fiber walks provide a base from which to model both the extension and expansion of physical biological objects with finite thickness 
Revised:  Hence, fiber walks provide a base from which to model both the extension and expansion of physical biological objects with finite thickness .
Edit intent: fluency
Original:  Scaling parameters of transitions can in principle be derived from  industrial dynamics, technology turnover rates and technology characteristics.
Revised:  In principle, scaling parameters of transitions can in principle be derived from industrial dynamics, technology turnover rates and technology characteristics.
Edit intent: fluency
Original:  Scaling parameters of transitions can in principle be derived from  industrial dynamics, technology turnover rates and technology characteristics.
Revised:  Scaling parameters of transitions can , however, be derived from industrial dynamics, technology turnover rates and technology characteristics.
Edit intent: coherence
Original:  Scaling parameters of transitions can in principle be derived from  industrial dynamics, technology turnover rates and technology characteristics.
Revised:  Scaling parameters of transitions can in principle be derived from knowledge of industrial dynamics, technology turnover rates and technology characteristics.
Edit intent: clarity
Original: Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade immunity acquired by the host population to previous virus strains.
Revised: Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains.
Edit intent: clarity
Original:  In our model, we simultaneously characterize antigenic and genetic evolution by including an evolutionary model in which antigenic location diffuses over a shared virus phylogeny.
Revised:  In our model, we simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny.
Edit intent: clarity
Original:  Using HI data for four lineages of influenza , encompassing influenza Asubtypes H3N2 and H1N1, and influenza Blineages Victoria and Yamagata, we determine average rates of antigenic drift for each lineage, as well as year-to-year variability in the rate of drift.
Revised:  Using HI data from influenza lineages A/ H3N2 and H1N1, and influenza Blineages Victoria and Yamagata, we determine average rates of antigenic drift for each lineage, as well as year-to-year variability in the rate of drift.
Edit intent: clarity
Original:  Using HI data for four lineages of influenza , encompassing influenza Asubtypes H3N2 and H1N1, and influenza Blineages Victoria and Yamagata, we determine average rates of antigenic drift for each lineage, as well as year-to-year variability in the rate of drift.
Revised:  Using HI data for four lineages of influenza , encompassing influenza Asubtypes H3N2 and H1N1, B/Victoria and B/ Yamagata, we determine average rates of antigenic drift for each lineage, as well as year-to-year variability in the rate of drift.
Edit intent: coherence
Original:  Using HI data for four lineages of influenza , encompassing influenza Asubtypes H3N2 and H1N1, and influenza Blineages Victoria and Yamagata, we determine average rates of antigenic drift for each lineage, as well as year-to-year variability in the rate of drift.
Revised:  Using HI data for four lineages of influenza , encompassing influenza Asubtypes H3N2 and H1N1, and influenza Blineages Victoria and Yamagata, we determine patterns of antigenic drift for each lineage, as well as year-to-year variability in the rate of drift.
Edit intent: clarity
Original:  We investigate the selective underpinnings for differing antigenic dynamics across lineages and show that A/H3N2 benefits from both a higher influx of new antigenic mutations and also from more efficient conversion of antigenic variation into fixed differences .
Revised:  We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage .
Edit intent: clarity
Original:  This work does much to elucidate the antigenic dynamics of influenza lineages, but also allows for substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution.
Revised:  This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution.
Edit intent: clarity
Original:  We use data on the initial rate of increase of the prevalence of HIV  and the life expectancy of people living with HIV before ARTbecame available to estimate R0 for countries in Africa.
Revised:  We use data on the rate at which the prevalence of HIV and the life expectancy of people living with HIV before ARTbecame available to estimate R0 for countries in Africa.
Edit intent: clarity
Original:  Frequently one applies cluster analysis in order to identify biologically interesting subgroups.
Revised:  In biomedical applications, one frequently applies cluster analysis in order to identify biologically interesting subgroups.
Edit intent: clarity
Original:  Conventional clustering methods often fail to identify such subgroups, particularly when there are a large number of high-variance features in the data set.
Revised:  Conventional clustering methods generally do not identify such subgroups, particularly when there are a large number of high-variance features in the data set.
Edit intent: clarity
Original:  We describe a modification of the sparse clustering method of Witten and Tibshirani (2010) that can be used to identify such secondary clusters or clusters associated with an outcome of interest.
Revised:  A modification of sparse clustering can be used to identify such secondary clusters or clusters associated with an outcome of interest.
Edit intent: clarity
Original:  We show that this method can correctly identify such clusters of interest in several simulation scenarios.
Revised:  This method correctly identifies such clusters of interest in several simulation scenarios.
Edit intent: clarity
Original:  The method is also applied to a large case-control study of TMD and a leukemia microarray data set.
Revised:  The method is also applied to a large prospective cohort study of temporomandibular disorders and a leukemia microarray data set.
Edit intent: clarity
Original:  The NetworGame algorithm is downloadable from here: www.  linkgroup.hu /NetworGame.php
Revised:  The NetworGame algorithm is downloadable from here: www. linkgroup.hu 
Edit intent: coherence
Original: %DIFDELCMD < {\em %%% Interactive proof systems (IP) are very powerful-languages they can accept form exactly PSPACE.
Revised: %DIFDELCMD < {\em %%% (IP) are very powerful-languages they can accept form exactly PSPACE.
Edit intent: clarity
Original:  So far this was explored for the case that verifiers are%DIFDELCMD < {\em %DIFDELCMD < %%% two-way probabilistic finite automata (Dwork and Stockmayer, 1990) and%DIFDELCMD < {\em %DIFDELCMD < %%% one-way quantum finite automata as well as%DIFDELCMD < {\em %%% two-way quantum finite automata (Nishimura and Yamakami, 2009).
Revised:  So far this was explored for the case that verifiers are%DIFDELCMD < {\em %DIFDELCMD < %%% (Dwork and Stockmayer, 1990) and%DIFDELCMD < {\em %DIFDELCMD < %%% one-way quantum finite automata as well as%DIFDELCMD < {\em %%% two-way quantum finite automata (Nishimura and Yamakami, 2009).
Edit intent: clarity