wanyu/IteraTeR_full_sent huggingface dataset:
Original:  This paper presents a theoretical computational method - an improved LBFGS Quasi-Newtonian mathematical optimization method - to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view  .
Revised:  This paper presents a theoretical computational method - an improved LBFGS Quasi-Newtonian mathematical optimization method - to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view . Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field .
Edit intent: coherence
Original:  Such deformation is shown to have a great contribution on the capturing process, first stage of any translocation phenomena. With a multiscale hybrid simulation (LB-MD)  it is shown that an effective deformation before reaching the pore occurs which facilitates the process of finding the entrance for the end monomers  .
Revised:  With a multi-scale hybrid simulation (LB-MD) it is shown that an effective deformation before reaching the pore occurs which facilitates the process of finding the entrance for the end monomers .
Edit intent: coherence
Original:  With a multiscale hybrid simulation (LB-MD)  it is shown that an effective deformation before reaching the pore occurs which facilitates the process of finding the entrance for the end monomers  .
Revised:  With a multiscale hybrid simulation (LB-MD) , it is shown that an effective deformation before reaching the pore occurs which facilitates the process of finding the entrance for the end monomers .
Edit intent: fluency
Original:  With a multiscale hybrid simulation (LB-MD)  it is shown that an effective deformation before reaching the pore occurs which facilitates the process of finding the entrance for the end monomers  .
Revised:  With a multiscale hybrid simulation (LB-MD) it is shown that an effective deformation before reaching the pore occurs which facilitates the process of finding the entrance for the end monomers . We also highlight the role of long range hydrodynamic interactions via comparison of the LB-MD results with those obtained using a Langevin thermostat instead of the LB solver .
Edit intent: meaning-changed
Original:   The paper introduces the numeraire property through the notion of expected relative return and shows that drawdown-constrained strategies with the numeraire property exist and are unique, but may depend on the financial planning horizon.
Revised:  We suggest to use path-wise growth optimality as the decision criterion and encode preferences through restrictions on the class of admissible wealth processes. Specifically, the investor is only interested in strategies which satisfy a given linear drawdown constraint. The paper introduces the numeraire property through the notion of expected relative return and shows that drawdown-constrained strategies with the numeraire property exist and are unique, but may depend on the financial planning horizon.
Edit intent: meaning-changed
Original:  We explicitly characterize the growth-optimal strategy and show that it enjoys the numeraire property within the class of investments satisfying the drawdown constraint , when sampled at the times of its maximum and asymptotically as the time-horizon becomes distant . Finally , it is established that the asymptotically growth-optimal strategy is obtained as limit of numeraire strategies on finite horizons.
Revised:  We explicitly characterize the growth-optimal strategy and show that it enjoys the numeraire property within the class of investments satisfying the drawdown constraint , when sampled at the times of its maximum and asymptotically as the time-horizon becomes distant , the drawdown-constrained numeraire portfolio is given explicitly through a model-independent transformation of the unconstrained numeraire portfolio. Further , it is established that the asymptotically growth-optimal strategy is obtained as limit of numeraire strategies on finite horizons.
Edit intent: meaning-changed
Original:  Furthermore, homology class number and size have a high degree of universality, depending on genome size only and not on genome-specific features. These "genomic laws" can be regarded as evolutionary constraints on the growth mechanism of genomes. We define a statistical model describing the joint growth of the network and the partitioning of nodes into homology classesunder the constraint of a stochastic class-expansion/innovation model based on the "Chinese restaurant process", and we study this model through a combined mean-field and simulation approach.
Revised:  Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two objects are intrinsically linked. Here, we first introduce a statistical model describing the joint growth of the network and the partitioning of nodes into homology classesunder the constraint of a stochastic class-expansion/innovation model based on the "Chinese restaurant process", and we study this model through a combined mean-field and simulation approach.
Edit intent: clarity
Original:  We define a statistical model describing the joint growth of the network and the partitioning of nodes into homology classesunder the constraint of a stochastic class-expansion/innovation model based on the "Chinese restaurant process", and we study this model through a combined mean-field and simulation approach.
Revised:  We define a statistical model describing the joint growth of the network and the partitioning of nodes into classes, which is studied through a combined mean-field and simulation approach.
Edit intent: coherence
Original:  Additionally, we define model variants that allow to study the age dependency of interactions under different prescriptions of duplication-divergence growth. Comparing with empirical data , we show that the model reproduces the observed universal behavior allowing a variant-independent fit of parameters.
Revised:  We then employ this unified framework to address the specific issue of the age dependence of protein interactions, through the definition of three different node wiring/divergence schemes. Comparison with empirical data , we show that the model reproduces the observed universal behavior allowing a variant-independent fit of parameters.
Edit intent: clarity
Original:  Comparing with empirical data , we show that the model reproduces the observed universal behavior allowing a variant-independent fit of parameters. This analysis also indicates that an age-dependent duplication move appears to be necessary for reproducing the basic network topological observables together with the age correlation between interacting nodes visible in empirical data  .
Revised:  Comparing with empirical data indicates that an age-dependent duplication move appears to be necessary for reproducing the basic network topological observables together with the age correlation between interacting nodes visible in empirical data .
Edit intent: coherence
Original:  This analysis also indicates that an age-dependent duplication move appears to be necessary for reproducing the basic network topological observables together with the age correlation between interacting nodes visible in empirical data  .
Revised:  This analysis also indicates that an age-dependent duplication move appears to be necessary for reproducing the basic network topological observables together with the age correlation between interacting nodes visible in empirical data . We also discuss the possibility of nontrivial joint partition/topology observables .
Edit intent: meaning-changed
Original:  To show how our symmetrization scheme works, we will present some numerical results applying (path-independent) Euler-Maruyama approximation to our scheme, comparing them with the path-dependent Euler-Maruyama scheme when the underlying process follows Black-Scholes and some CEVmodels .
Revised:  To show how our symmetrization scheme works, we will present some numerical results applying (path-independent) Euler-Maruyama approximation to our scheme, comparing them with the path-dependent Euler-Maruyama scheme when the model is of the Black-Scholes and some CEVmodels .
Edit intent: clarity
Original:  To show how our symmetrization scheme works, we will present some numerical results applying (path-independent) Euler-Maruyama approximation to our scheme, comparing them with the path-dependent Euler-Maruyama scheme when the underlying process follows Black-Scholes and some CEVmodels .
Revised:  To show how our symmetrization scheme works, we will present some numerical results applying (path-independent) Euler-Maruyama approximation to our scheme, comparing them with the path-dependent Euler-Maruyama scheme when the underlying process follows Black-Scholes , CEV, Heston, and (\lambda) -SABR, respectively .
Edit intent: meaning-changed
Original:  In a recent study \mbox{%DIFAUXCMD DBB , it was proposed to revert this point of view and consider simulations as made of dozens of sequences of eigenvalue problems; each sequence groups together eigenproblems with equal%DIFDELCMD < {\bf %%% k -vectors and an increasing outer-iteration cycle index \ell.
Revised:  In a recent study \mbox{%DIFAUXCMD DBB , it was %DIFDELCMD < {\bf %%% k -vectors and an increasing outer-iteration cycle index \ell.
Edit intent: coherence
Original:  each sequence groups together eigenproblems with equal%DIFDELCMD < {\bf %%% k -vectors and an increasing outer-iteration cycle index \ell. From this different standpoint it was possible to demonstrate that, contrary to belief, successive eigenproblems in a sequence are strongly correlated with one another.
Revised:  each sequence groups together eigenproblems with equal%DIFDELCMD < {\bf %%% k demonstrated that, contrary to belief, successive eigenproblems in a sequence are strongly correlated with one another.
Edit intent: coherence
Original:  In particular, by tracking the evolution of subspace angles between eigenvectors of successive eigenproblems, it was shown that these angles decrease noticeably after the first few iterations and become close to collinear : the closer to convergence the stronger the correlation becomes .
Revised:  In particular, by monitoring the subspace angles between eigenvectors of successive eigenproblems, it was shown that these angles decrease noticeably after the first few iterations and become close to collinear : the closer to convergence the stronger the correlation becomes .
Edit intent: clarity
Original:  In particular, by tracking the evolution of subspace angles between eigenvectors of successive eigenproblems, it was shown that these angles decrease noticeably after the first few iterations and become close to collinear : the closer to convergence the stronger the correlation becomes .
Revised:  In particular, by tracking the evolution of subspace angles between eigenvectors of successive eigenproblems, it was shown that these angles decrease noticeably after the first few iterations and become close to collinear .
Edit intent: clarity
Original: The nonlinear elastic properties of fibrin networks are crucial for normal blood clotting . Here, we show that the extraordinary strain-stiffening response of fibrin clots reflects the hierarchical architecture of the fibrin fibers , which are bundles of wormlike protofibrils .
Revised: The nonlinear elastic properties of fibrin networks are crucial for normal blood clotting , protofibrils self-assemble and bundle to form networks of semiflexible fibers. Here we show that the extraordinary strain-stiffening response of fibrin clots reflects the hierarchical architecture of the fibrin fibers , which are bundles of wormlike protofibrils .
Edit intent: meaning-changed
Original:  Here, we show that the extraordinary strain-stiffening response of fibrin clots reflects the hierarchical architecture of the fibrin fibers , which are bundles of wormlike protofibrils .
Revised:  Here, we show that the extraordinary strain-stiffening response of fibrin networks is a direct reflection of the hierarchical architecture of the fibrin fibers , which are bundles of wormlike protofibrils .
Edit intent: clarity
Original:  At high stress, the protofibrils contribute independently to the network elasticity, which may reflect a decoupling of the tight bundle structure.
Revised:  We demonstrate that the tightness of coupling between protofibrils in the fibers can be tuned by the degree of enzymatic intermolecular crosslinking by the coagulation Factor XIII. Furthermore, at high stress, the protofibrils contribute independently to the network elasticity, which may reflect a decoupling of the tight bundle structure.
Edit intent: meaning-changed
Original:   Our data analysis of six major indices suggests that the actual interaction structure is mathematically equivalent to an Ising model on a complete graph with gaussian interaction strengths scaling as the inverse of the system size.
Revised:  This is done with an approach only based on empirical data of price returns. Our data analysis of six major indices suggests that the actual interaction structure is mathematically equivalent to an Ising model on a complete graph with gaussian interaction strengths scaling as the inverse of the system size.
Edit intent: meaning-changed
Original:  Spin glass models have been applied and gave some valuable results but at the price of restrictive assumptions on the market dynamics or they are agent-based models with rules designed in order to recover some empirical behaviors .
Revised:  Spin glass models have been applied and gave some valuable results but at the price of restrictive assumptions on the market dynamics or they are agent-based models with rules designed in order to recover some empirical behaviours .
Edit intent: fluency
Original:  We show that for this model with cooperative interaction all conformations with minimal energy are combinations of lattice models of alpha-helix and beta-strand. We show that for lattice polymers of the length not longer that 38 monomers we can describe all conformations with minimal energy.
Revised:  We show that for this model with cooperative interaction all conformations with minimal energy are combinations of lattice models of alpha--helix and beta--strand. Moreover for lattice polymers of the length not longer that 38 monomers we can describe all conformations with minimal energy.
Edit intent: coherence
Original:  Besides the model can be considered mathematically very simple, it was able to improve significantly the performance of agents operating with real financial data , as will be showed in this paper . Based on the results obtained, and also on the very intuitive logic of our model, we believe that the index proposed here can be very useful to help investors on the activity of determining ideal price ranges for buying and selling stocks in the financial market.
Revised:  Besides the model can be considered mathematically very simple, it was able to improve significantly the performance of agents operating with real financial data . Based on the results obtained, and also on the very intuitive logic of our model, we believe that the index proposed here can be very useful to help investors on the activity of determining ideal price ranges for buying and selling stocks in the financial market.
Edit intent: coherence
Original: We study physical limits of chemical sensing by a single chemotactic cell with cooperative chemoreceptors on the cell surface .
Revised: Most sensory cells use cross-membrane chemoreceptors to detect chemical signals in the environment. The biochemical properties and URLanization of chemoreceptors play important roles in achieving and maintaining sensitivity and accuracy of chemical sensing. Here we investigate the effects of receptor cooperativity and adaptation on the limits of gradient sensing. We study a single cell with aggregated chemoreceptor arrays on the cell surface .
Edit intent: clarity
Original: We study physical limits of chemical sensing by a single chemotactic cell with cooperative chemoreceptors on the cell surface . We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Revised: We study physical limits of chemical sensing by a single chemotactic cell with cooperative chemoreceptors on the cell surface and derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Edit intent: fluency
Original:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Revised:  We derive general formula to the limits for gradient sensing from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Edit intent: clarity
Original:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Revised:  We derive general formula for the gradient sensing limit from the uncertainty of instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Edit intent: fluency
Original:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Revised:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity . In comparison to independent receptors, we find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Edit intent: meaning-changed
Original:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Revised:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptative receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Edit intent: fluency
Original:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Revised:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit in a chemical concentration range determined by the biochemical properties of ligand-receptor binding and ligand-induced receptor activity . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Edit intent: meaning-changed
Original:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Revised:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptative receptors are beneficial to gradient sensing under a broad range of background concentrations.
Edit intent: clarity
Original:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing under a broad range of background concentrations.
Revised:  We derive general formula for the gradient sensing limit from the uncertainty in instantaneous receptor activity configurations and find that cooperativity by non-adaptive receptors could significantly lower the sensing limit at the biochemically-relevant regime of balanced free energy difference between active and inactive receptor states . Cooperativity by adaptive receptors are beneficial to gradient sensing within a broad range of background concentrations.
Edit intent: clarity