wanyu/IteraTeR_v2 huggingface dataset:
Original:  Thus, SHAPE-directed RNA modeling is not always accurate , and helix-by-helix confidence estimates, as described herein, may be critical for interpreting results from this powerful methodology.
Revised:  Thus, SHAPE-directed RNA modeling is not always unambiguous , and helix-by-helix confidence estimates, as described herein, may be critical for interpreting results from this powerful methodology.
Edit intent: clarity
Original:  We introduce a one-dimensional model with a steady accumulation of beneficial mutations.
Revised:  We introduce a one dimensional model with a steady accumulation of beneficial mutations.
Edit intent: fluency
Original:  These proteins are so tightly packed that their excluded area interactions can alter the free energy landscape associated with their conformational degrees of freedom .
Revised:  These proteins are so tightly packed that their excluded area interactions can alter the free energy landscape associated with their conformational degrees of freedomin vivo .
Edit intent: clarity
Original:  As a specific case study in these effects , we consider the impact of crowding on the gating tension for mechanosensitive channels.
Revised:  As a specific case study in this effect , we consider the impact of crowding on the gating tension for mechanosensitive channels.
Edit intent: fluency
Original:  We show that crowding can alter the gating energies by more than \approx 2  k_BT  , a substantial fraction of the gating energies themselves in some cases  .
Revised:  We show that crowding can alter the gating energies by more than 2 k_BT , a substantial fraction of the gating energies themselves in some cases .
Edit intent: clarity
Original:  We show that crowding can alter the gating energies by more than \approx 2  k_BT  , a substantial fraction of the gating energies themselves in some cases  .
Revised:  We show that crowding can alter the gating energies by more than \approx 2 k_BT , a substantial fraction of the total gating energies in some cases .
Edit intent: clarity
Original:  If driveduring female meiosis one is common, our model explains the high genome-wide female recombination rates, the disproportionately elevated female recombination rates near centromeresand other puzzling features of female meiosis as adaptive mechanisms to suppress female-limited meiotic drive systems .
Revised:  If driveduring female meiosis one is common, our model explains the high genome-wide female recombination rates, particularly around centromeres, should be a common outcome of meiotic drive. We discuss how selection to modify the efficacy of meiotic drive may contribute to commonly observed patterns of sex-differences in recombination .
Edit intent: clarity
Original: The Quantum Substate Theorem due to Jain, Radhakrishnan, and Sen ( 2009 ) gives us a powerful operational interpretation of  the observational divergence of two quantum states, a quantity that is closely related to their relative entropy.
Revised: The Quantum Substate Theorem due to Jain, Radhakrishnan, and Sen ( 2009 ) gives us a powerful operational interpretation of the observational divergence of two quantum states, a quantity that is related to their relative entropy.
Edit intent: clarity
Original:  Informally, the theorem states that if the observational divergence between two quantum states rho, sigma is small, then there is a quantum state rho' close to rho in trace norm , such that rho' when scaled down by a small factor becomes a substate of sigma.
Revised:  Informally, the theorem states that if the observational divergence between two quantum states rho, sigma is small, then there is a quantum state rho' close to rho in trace distance , such that rho' when scaled down by a small factor becomes a substate of sigma.
Edit intent: clarity
Original:  We present a new proof of this theorem.
Revised:  We present new proofs of this theorem.
Edit intent: clarity
Original:  An inductively defined small-step semantics and a coinductively definedbig step semantics are shown to produce identical outcomes, both in call-by-value and in call-by-name.
Revised:  Small-step and a coinductively definedbig step semantics are shown to produce identical outcomes, both in call-by-value and in call-by-name.
Edit intent: clarity
Original:  An inductively defined small-step semantics and a coinductively definedbig step semantics are shown to produce identical outcomes, both in call-by-value and in call-by-name.
Revised:  An inductively defined small-step semantics and a coinductively definedbig step semantics are shown to produce identical outcomes, both in call-by- value and in call-by-name.
Edit intent: fluency
Original: By constraining the possible values of the proportion of null hypotheses that are true, the local false discovery rate (LFDR) can be estimated using as few as one comparison.
Revised: By restricting the possible values of the proportion of null hypotheses that are true, the local false discovery rate (LFDR) can be estimated using as few as one comparison.
Edit intent: fluency
Original:  Results of extensive simulations of this model show the existence of four phases with regards to the rates of both the influx of resources and the cell growth.
Revised:  Results of extensive simulations of this model show the existence of four phases with regard to the rates of both the influx of resources and the cell growth.
Edit intent: fluency
Original:  every unhappy family is unhappy in its own way ".
Revised:  every unhappy family is unhappy in its own way ."
Edit intent: fluency
Original:  In this paper we introduce the Anna Karenina principle as a principle that can explain success in science.
Revised:  In this paper we introduce the Anna Karenina principle as a concept that can explain success in science.
Edit intent: clarity
Original: In the paper is discussed software model of a reversible processor ReveR with stack.
Revised: A software model of a reversible processor ReveR with stack.
Edit intent: clarity
Original:  It is described architecture, minimal set of elementary reversible operations together with implementation of basic control flow structures and procedures calls using simple assembler language  .
Revised:  It is described architecture, minimal set of elementary reversible operations together with an implementation of the basic control flow structures and procedures calls using simple assembler language .
Edit intent: fluency
Original:  It is described architecture, minimal set of elementary reversible operations together with implementation of basic control flow structures and procedures calls using simple assembler language  .
Revised:  It is described architecture, minimal set of elementary reversible operations together with implementation of basic control flow structures and procedures calls using simple assembler language are described .
Edit intent: clarity
Original:  In this study, we adopt a different approach whereby macroscopic flows are redirected throughout the bioreactor along patterned channels in the scaffold that result in optimized shear stress distributions  .
Revised:  In this study, we have adopted a different approach whereby macroscopic flows are redirected throughout the bioreactor along patterned channels in the scaffold that result in optimized shear stress distributions .
Edit intent: fluency
Original:  In this study, we adopt a different approach whereby macroscopic flows are redirected throughout the bioreactor along patterned channels in the scaffold that result in optimized shear stress distributions  .
Revised:  In this study, we adopt a different approach whereby flows are redirected throughout the bioreactor along patterned channels in the scaffold that result in optimized shear stress distributions .
Edit intent: clarity
Original:  In this study, we adopt a different approach whereby macroscopic flows are redirected throughout the bioreactor along patterned channels in the scaffold that result in optimized shear stress distributions  .
Revised:  In this study, we adopt a different approach whereby macroscopic flows are redirected throughout the bioreactor along channels patterned in the porous scaffold to yield shear stress distributions .
Edit intent: clarity
Original:  A topology optimization algorithm coupled to effective-medium Lattice Boltzmann simulations was devised to find an optimal channel design that yields a target shear stress that is uniformly distributed throughout the scaffold .
Revised:  A topology optimization algorithm coupled to computational fluid dynamics simulations was devised to find an optimal channel design that yields a target shear stress that is uniformly distributed throughout the scaffold .
Edit intent: clarity
Original:  A topology optimization algorithm coupled to effective-medium Lattice Boltzmann simulations was devised to find an optimal channel design that yields a target shear stress that is uniformly distributed throughout the scaffold .
Revised:  A topology optimization algorithm coupled to effective-medium Lattice Boltzmann simulations was devised to this end .
Edit intent: clarity
Original:  The ability of topology optimization to alter the shear stress distribution is implemented in experiments where magnetic resonance imaging (MRI) is used to image the flow field.
Revised:  The ability of topology optimization to alter the shear stress distribution is implemented in experiments where magnetic resonance imaging (MRI) readouts of the flow field.
Edit intent: clarity
Original:  (The same result, but with a bikernel to Max-r-LIn2-AA [k], is valid for a wide family of constraint satisfaction problems.)
Revised:  (The same result, but with a bikernel to Max-r-Lin2-AA [k], is valid for a wide family of constraint satisfaction problems.)
Edit intent: fluency
Original:  (The same result, but with a bikernel to Max-r-Lin2-AA k%DIFDELCMD < ]%%% , is valid for a wide family of constraint satisfaction problems.)
Revised:  k%DIFDELCMD < ]%%% , is valid for a wide family of constraint satisfaction problems.)
Edit intent: coherence
Original:  (The same result, but with a bikernel to Max-r-Lin2-AA k%DIFDELCMD < ]%%% , is valid for a wide family of constraint satisfaction problems.)
Revised:  (The same result, but with a bikernel to Max-r-Lin2-AA %DIFDELCMD < ]%%% , is valid for a wide family of constraint satisfaction problems.)
Edit intent: clarity
Original:  We show applicability of the lower bound by giving a new proof of the Edwards-Erd{\H o}s bound (each connected graph on n vertices and m edges has a bipartite subgraph with at least m/2 + (n-1)/4 edges) and proving its generalization.
Revised:  We show applicability of the lower bound by giving a new proof of the Edwards-Erd{\H o}s bound (each connected graph on n vertices and m edges has a bipartite subgraph with at least m/2 + (n-1)/4 edges) and obtaining a generalization.
Edit intent: clarity
Original: Tight-spans of metrics were first introduced by Isbell in 1964 and rediscovered and studied by others, most notably by Dress  who gave them this name.
Revised: Tight-spans of metrics were first introduced by Isbell in 1964 and rediscovered and studied by others, most notably by Dress , who gave them this name.
Edit intent: fluency
Original:  Our coder aims at reproducing the main steps of the visual stimulus processing in the mammalians retina taking into account its time behavior.
Revised:  Our coder aims at reproducing the main steps of the visual stimulus processing in the mammalian retina taking into account its time behavior.
Edit intent: fluency
Original:  Also, compared to the JPEG standards, our decoded images do not show annoying artefacts such as ringing and block effects.
Revised:  Also, our decoded images do not show annoying artefacts such as ringing and block effects.
Edit intent: clarity
Original:  As a whole, this article shows how to capture the main properties of a biological system, here the retina, in order to the design a new efficient coder.
Revised:  As a whole, this article shows how to capture the main properties of a biological system, here the retina, in order to design a new efficient coder.
Edit intent: fluency
Original: The primary visual cortex of many mammals contains a continuous representation of visual space, with an aperiodic map of orientation preferences superimposed.
Revised: The primary visual cortex of many mammals contains a continuous representation of visual space, with a roughly repetitive aperiodic map of orientation preferences superimposed.
Edit intent: clarity
Original:  Here, we ask whether one of the most prominent models for the optimization of cortical maps, the elastic net (EN) model can reproduce these universal statistics .
Revised:  Here, we examine whether one of the most prominent models for the optimization of cortical maps, the elastic net (EN) model can reproduce these universal statistics .
Edit intent: clarity
Original:  Here, we ask whether one of the most prominent models for the optimization of cortical maps, the elastic net (EN) model can reproduce these universal statistics .
Revised:  Here, we ask whether one of the most prominent models for the optimization of cortical maps, the elastic net (EN) model , can reproduce this common design .
Edit intent: clarity
Original:  The EN model generates representations which optimally trade off stimulus space coverage and map continuity.
Revised:  The EN model generates representations which optimally trade of stimulus space coverage and map continuity.
Edit intent: fluency
Original:  While this model has been used in numerous numerical studies, no analytical results about its optimal solutions have been obtained so far.
Revised:  While this model has been used in numerous studies, no analytical results about its optimal solutions have been obtained so far.
Edit intent: clarity
Original:  We present a mathematical approach to analytically calculate the optimal cortical representations predicted by the EN model for the joint mapping of stimulus position and orientation.
Revised:  We present a mathematical approach to analytically calculate the cortical representations predicted by the EN model for the joint mapping of stimulus position and orientation.
Edit intent: clarity
Original:  We find that in all previously studied regimes, optimal OPM layouts are perfectly periodic.
Revised:  We find that in all previously studied regimes, predicted OPM layouts are perfectly periodic.
Edit intent: clarity
Original:  An unbiased search through the EN parameter space identifies a novel regime of aperiodic solutions with pinwheel densities lower than found in experiments.
Revised:  An unbiased search through the EN parameter space identifies a novel regime of aperiodic OPMs with pinwheel densities lower than found in experiments.
Edit intent: clarity
Original:  In an extreme limit, aperiodic solutions quantitatively resembling experimental observations become optimal . Stabilization of these layouts results from strong nonlocal interactions rather than from a coverage-continuity-compromise.
Revised:  In an extreme limit, aperiodic OPMs quantitatively resembling experimental observations become optimal . Stabilization of these layouts results from strong nonlocal interactions rather than from a coverage-continuity-compromise.
Edit intent: clarity
Original:  In an extreme limit, aperiodic solutions quantitatively resembling experimental observations become optimal . Stabilization of these layouts results from strong nonlocal interactions rather than from a coverage-continuity-compromise.
Revised:  In an extreme limit, aperiodic solutions quantitatively resembling experimental observations emerge . Stabilization of these layouts results from strong nonlocal interactions rather than from a coverage-continuity-compromise.
Edit intent: clarity
Original:  Our results demonstrate that optimization models for stimulus representations dominated by nonlocal suppressive interactions are in principle capable of correctly predicting the universal OPM statistics .
Revised:  Our results demonstrate that optimization models for stimulus representations dominated by nonlocal suppressive interactions are in principle capable of correctly predicting the common OPM design .
Edit intent: clarity
Original: Tree-depth is a parameter introduced under several names as a measure of sparsity of a graph.
Revised: The tree-depth is a parameter introduced under several names as a measure of sparsity of a graph.
Edit intent: clarity
Original:  We compute asymptotic values of  tree-depth of random graphs.
Revised:  We compute asymptotic values of the tree-depth of random graphs.
Edit intent: fluency
Original:  For dense graphs, p =\omega ( 1/n ) , the tree-depth of a random graph G is a.a.s. td(G)= n-o(n ). Random graphs with p=c/n, have a.a.s. linear tree-depth when c>1, the tree-depth is \Theta ( n) when c=1 and \Theta (\log\log n) for c<1.
Revised:  For dense graphs, p =\omega ( 1/n , the tree-depth of a random graph G is a.a.s. td(G)= n-o(n ). Random graphs with p=c/n, have a.a.s. linear tree-depth when c>1, the tree-depth is \Theta ( n) when c=1 and \Theta (\log\log n) for c<1.
Edit intent: fluency
Original:  For dense graphs, p =\omega ( 1/n ) , the tree-depth of a random graph G is a.a.s. td(G)= n-o(n ). Random graphs with p=c/n, have a.a.s. linear tree-depth when c>1, the tree-depth is \Theta ( n) when c=1 and \Theta (\log\log n) for c<1.
Revised:  For dense graphs, p =\omega ( 1/n ) , the tree-depth of a random graph G is a.a.s. td(G)= n-o(n ). Random graphs with p=c/n, have a.a.s. linear tree-depth when c>1, the tree-depth is Theta (log n) when c=1 and \Theta (\log\log n) for c<1.
Edit intent: clarity
Original: The network traffic matrix is a kind of flow-level Internet traffic data and is widely applied to network operation and management.
Revised: The network traffic matrix is widely used in network operation and management.
Edit intent: clarity
Original:  It is a crucial problem to analyze the composition and structure of traffic matrix;
Revised:  It is therefore of crucial importance to analyze the composition and structure of traffic matrix;
Edit intent: clarity
Original:  some mathematical approaches such as Principal Component Analysis (PCA) were used to handle that problem .
Revised:  some mathematical approaches such as Principal Component Analysis (PCA) were proposed .
Edit intent: clarity
Original:  In this paper, we first argue that PCA performs poorly for analyzing traffic matrixes polluted by large volume anomalies,  then propose a new composition model of the network traffic matrix.
Revised:  In this paper, we first argue that PCA performs poorly for analyzing traffic matrix that is polluted by large volume anomalies, then propose a new composition model of the network traffic matrix.
Edit intent: clarity
Original:  In this paper, we first argue that PCA performs poorly for analyzing traffic matrixes polluted by large volume anomalies,  then propose a new composition model of the network traffic matrix.
Revised:  In this paper, we first argue that PCA performs poorly for analyzing traffic matrixes polluted by large volume anomalies, and then propose a new composition model of the network traffic matrix.
Edit intent: coherence
Original:  In this paper, we first argue that PCA performs poorly for analyzing traffic matrixes polluted by large volume anomalies,  then propose a new composition model of the network traffic matrix.
Revised:  In this paper, we first argue that PCA performs poorly for analyzing traffic matrixes polluted by large volume anomalies, then propose a new decomposition model for the network traffic matrix.
Edit intent: clarity
Original:  At last, further discussions on the deterministic traffic and the noise trafficare carried out.
Edit intent: coherence
Original:  Our study gives a proper method for traffic matrix structure analysis, which has a defense against the pollution of large volume anomalies.
Revised:  Our study develops a novel method for the problem of structural analysis of the traffic matrix, which is robust against pollution of large volume anomalies.
Edit intent: clarity
Original:  Incremental gradient algorithms (both deterministic and randomized) offer inexpensive iterations by sampling only subsets of the terms in the sum.
Revised:  Incremental gradient algorithms offer inexpensive iterations by sampling only subsets of the terms in the sum.
Edit intent: clarity
Original:  Rate of convergence analysis  and numerical experiments illustrate the potential for the approach .
Revised:  Rate of convergence analysis and numerical experiments illustrate its potential benefits .
Edit intent: clarity
Original:  Incremental gradient algorithms offer inexpensive iterations by sampling only subsets of the terms in the sum.
Revised:  Incremental gradient algorithms offer inexpensive iterations by sampling a subset of the terms in the sum.
Edit intent: clarity
Original:  In contrast, full gradient methods achieve steady convergence at the expense of evaluating the full objective and gradient on each iteration.
Revised:  In contrast, full-gradient methods achieve steady convergence at the expense of evaluating the full objective and gradient on each iteration.
Edit intent: fluency
Original:  Rate of convergence analysis shows that by controlling the size of the subsets in an incremental gradient algorithm, it is possible to maintain the steady convergence rates of full gradient methods.
Revised:  Rate-of-convergence analysis shows that by controlling the size of the subsets in an incremental gradient algorithm, it is possible to maintain the steady convergence rates of full gradient methods.
Edit intent: fluency
Original:  Rate of convergence analysis shows that by controlling the size of the subsets in an incremental gradient algorithm, it is possible to maintain the steady convergence rates of full gradient methods.
Revised:  Rate of convergence analysis shows that by controlling the sample size in an incremental gradient algorithm, it is possible to maintain the steady convergence rates of full gradient methods.
Edit intent: clarity
Original:  Rate of convergence analysis shows that by controlling the size of the subsets in an incremental gradient algorithm, it is possible to maintain the steady convergence rates of full gradient methods.
Revised:  Rate of convergence analysis shows that by controlling the size of the subsets in an incremental gradient algorithm, it is possible to maintain the steady convergence rates of full-gradient methods.
Edit intent: fluency
Original:  We detail a practical quasi-Newton implementation based on this approach , and numerical experiments illustrate its potential benefits.
Revised:  We detail a practical quasi-Newton implementation based on this approach . Numerical experiments illustrate its potential benefits.
Edit intent: coherence
Original:  Programing details along with optimization issues are discussed, followed by a comparison of performance on different devices.
Revised:  Programing details along with optimization issues are discussed, followed by a com- parison of performance on different devices.
Edit intent: fluency
Original:  Both methods has been compared with visualizing data to  external software - gnuplot.
Revised:  Both methods have been compared with visualizing data to external software - gnuplot.
Edit intent: fluency
Original:  Both methods has been compared with visualizing data to  external software - gnuplot.
Revised:  Both methods has been compared with visualizing data to an external software - gnuplot.
Edit intent: fluency
Original:  OpenCL/OpenGL interoperating method has been found the most appropriate to visualize  large set of data for which calculation itself is not very long.
Revised:  OpenCL/OpenGL interoperating method has been found the most appropriate to visualize any large set of data for which calculation itself is not very long.
Edit intent: clarity