Assessment of the accuracy of geometric tests of a linac used in external beam therapy is crucial for ensuring precise dose delivery. In this paper, a new simulation‐based method for assessing accuracy of such geometric tests is proposed and evaluated on a set of testing procedures.Linac geometry testing methods used in this study are based on an established design of a two‐module phantom. Electronic portal imaging device (EPID) images of fiducial balls contained in these modules can be used to automatically reconstruct linac geometry. The projection of the phantom modules fiducial balls onto the EPID detector plane is simulated for assumed nominal geometry of a linac. Then, random errors are added to the coordinates of the projections of the centers of the fiducial balls and the linac geometry is reconstructed from these data.Reconstruction is performed for a set of geometric test designs and it is shown how the dispersion of the reconstructed values of geometric parameters depends on the design of a geometric test. Assuming realistic accuracy of EPID image analysis, it is shown that for selected testing plans the reconstruction accuracy of geometric parameters can be significantly better than commonly used action thresholds for these parameters.Proposed solution has the potential to improve geometric testing design and practice. It is an important part of a fully automated geometric testing solution. This requirement may be met provided that the geometry of the beam agrees with the geometry defined in the treatment planning system (TPS).In practice, the nominal geometry of a linac as defined in TPS agrees with the real geometry of the device only to a limited accuracy. The discrepancies between a nominal and a real geometry have the source in the construction of linear accelerator components and especially in their enormous weights leading to flexing or sagging of the system components during gantry rotation.Each country has its own legislation or recommendations for the quality tests, for example, in a form of papers prepared by national societies of medical physicists which specify types of tests to perform, their frequency, and proposed tolerance values, based on international guidelines.A generic procedure for a geometric test  consists of positioning of a special phantom containing one or more radiopaque fiducial markers in a radiation beam, acquisition of MeV images of the phantom  images) and then—based on dedicated image analysis methods—determination of the quantities of interest like isocenter position, source to detector distance (SDD) etc.There are at least three weak points in this procedure. First, the EPID images offer limited resolution with a pixel size of only about 0.35 mm. The geometric tests are based on prior determination of the positions of the projection of the centers of phantom fiducials onto the EPID image plane. Consequently, the accuracy of the consecutive analysis steps and in particular accuracy of the estimation of geometric parameters are limited by the resolution of EPID detectors. Next, the EPID images are corrupted by noise and for this reason analysis of two projection images of a phantom acquired under exactly the same geometric settings may return different results of geometric testing. Finally, there is no systematic way for setting action thresholds for the values of the geometric parameters. In particular, without knowing how big the random errors introduced by an image noise and systematic errors introduced by limited EPID resolution are, it is not clear if the accuracy requirements can be met or, contrary, if the requirements are too loose posing a hazard of a malfunctioning device passing a test.This paper is an extension of a previous work22.1B = {kB: k = 1, 2, …, BN} of BN fiducial balls and the second one, mounted on a gantry head, contains a set C = {lC: l = 1, 2,..., CN} of CN fiducial balls.In this work, the process of projecting fiducial markers onto the EPID matrix is simulated, taking into account errors caused by finite resolution of the detector and noise inherently associated with imaging process. In the simulations, we assume that all the subsystems of a simulated device are set correctly, that is, there is no difference between nominal and actual device settings like gantry or collimator angle, SDD, jaw positions, and other. Acquisition of images of a multimodule multifiducial phantomQ denote a parameter which must be estimated during a geometrical testing of a linac . Q, like any other geometrical parameter, has some preset nominal value NQ, which is used to simulate the process of acquisition of phantom EPID images. We denote by MQ a value of Q estimated based on analysis of EPID images.Let MQ is a random variable sampled from some distribution with probability density function Qf where TP describes the testing procedure and σ is the standard deviation quantifying the uncertainty of the EPID image analysis. The procedure TP = {: i = 1, 2,..., ΘN, j = 1, 2,..., Nψ} of geometrical testing of a linac consists of a set of pairs of collimator angles iθ and gantry angles jψ. The testing procedure depends also on other geometrical settings like table position or rotation. These settings were fixed in the simulations, although both table translation and rotation can be determined from the projection images of the phantom used in the simulation.Due to inherent noise present in images captured by ionizing radiation detectors, kB and lC onto the EPID imaging plane are determined for each element of TP using nominal settings of a linac. It is assumed that the measured coordinates P(kB) and P(lC) of the projections of centers of kB and lC, respectively, onto the EPID imaging plane are random variables with a two‐dimensional symmetric Gaussian distribution centered at the nominal projection points of the centers of the ball markers and standard deviation equal to σ.The nominal coordinates of the projections of the centers of P(kB) and P(lC) of the projections of the centers of fiducial markers kB and lC for each element of TP, Q is recomputed from these data resulting in MQ. MQ differs from NQ to an extent that depends on how big the uncertainty σ is, on the phantom design  and on the testing procedure TP. While TP, B and C are a part of the designed testing procedure, the value of σ can be reduced by for example increasing the irradiation time or by increasing the resolution of the EPID detector matrix.Given the measured coordinates TP, B, C, and σ and repeating the simulation multiple times, we find the probability density function Qf of the measured values. MQ of Q. Qf is then used to determine how the selection of testing procedure TP, the phantom design B and C and the uncertainty of image analysis σ influence the accuracy of estimating Q.Fixing Further details concerning the simulations and reconstruction of the geometry of the linac are described in Data 2.2I, rotation axes of the collimator are determined for a sequence ψ = {ψ1, ψ2,..., Nψ} of angular positions of a gantry. Let these axes be denoted by R1, R2,..., NR. Then, the position of the isocenter is defined as follows:d is the distance from a point P to the axis Ri. Nominally, isocenter is located at the origin, that is, the point with coordinates . From the simulations, we determine the distribution of the distance from the nominal to the calculated position of the isocenter as well as distributions of the components of the calculated isocenter position. The reconstruction procedure is performed using Algorithm 2 from Data Radiation isocenter position. To find the radiation isocenter SDD is 180 cm. The value of SDD is calculated based on the isocenter position calculated using Algorithm 2 and equation of the detector plane obtained using Algorithm 4 from Data Source to detector distance, which is the distance from the source of the MeV radiation to the EPID detector plane. The nominal value of SAD), which is the distance from the source to the projection of the source onto the plane normal to the rotation axis of the collimator and containing the isocenter. The nominal value of SAD is 100 cm. It is calculated using isocenter position, reconstructed collimator axis and reconstructed radiation source position (see Algorithms 2 and 4).Source to axis distance , that is a vector parallel to the Y axis of the coordinate frame of the isocenter. First, positions of fiducial ball markers and radiation sources are collected for a set of gantry angles and collimator angles. Gantry rotation axis is estimated by calculating the extrinsic mean of directions of optimal rotations of collected points for different gantry angles , from 5 to 25 collimator angles . Random selection of gantry and collimator angles was also tested. The number of fiducial balls of phantom modules was varied from 4 to 8 for the collimator‐mounted module and from 6 to 10 for the table‐mounted module. The fiducial markers of the table‐mounted module were organized in parallel planes, at most four markers within one plane. All used markers had the radius of 3 mm. In any case it was checked that all the markers are projected onto EPID for every angular position of the gantry head contained in the testing plan and that their projections onto EPID do not overlap . In the case of a collimator‐mounted module, the ball markers are projected onto EPID provided that they are within the radiation field. The fiducial markers of the collimator‐mounted module were also organized in parallel planes, at most three markers within one plane. The standard deviation of the uncertainty of determination of the projection of the phantom balls centers was varied in the range from 0.1 to 0.5 mm. While the actual size of an EPID pixel depends on an EPID model, currently, the smallest size of an EPID pixel is approximately equal to 0.35 mm.In Fig. In Tables SDD was decreased from 180 cm as in previous numerical experiments to 140 cm. The simulations were run for gantry and collimator angles incremented by 5°. In Table In the final experiment, we considered a case of a bigger phantom, occupying a cuboid of size 26 cm × 18 cm × 26 cm, containing 18 fiducial balls in the table‐mounted module and eight fiducial balls in the collimator‐mounted module. The balls of the table‐mounted module were distributed along a spiral pattern whose axis was parallel to the axis of a gantry rotation. The fiducial markers of the collimator‐mounted module were contained in parallel planes, at most four markers within each plane. The configuration of both modules is depicted in Fig. 4In this paper, we demonstrated how the dispersion of geometric parameters derived from the projection images of a specialized phantom depends on the design of a testing procedure and the design of the phantom. The simulations were run assuming that there is an error in estimating the coordinates of the projections of phantom markers onto the EPID detector plane. This error was modeled as a Gaussian random variable with standard deviation ranging from 0.1 to 0.5 mm. The smallest size of pixel in currently used EPID devices is approximately equal to 0.35 mm. Given the state‐of‐the‐art image analysis methods like circle Hough transform and knowing the approximate position of each marker already from the nominal settings of a linac, it can be safely agreed that the error in determining the coordinates of the projections of phantom markers onto an EPID detector plane will be never greater than ±2 pixels. For reference, Du and YangThe construction of phantom modules together with the procedure used in these simulations guarantee that the procedure is not influenced by certain types of error that have to be taken into account in standard geometry tests.α is reduced by approximately 40%. By increasing the number of markers within the collimator‐mounted module by a factor of two, the error α is reduced by a factor of three. These dependencies are clear as the axis of collimator rotation is determined from the coordinates of the markers of the collimator‐mounted module. To determine these coordinates, the projections of the markers of the table‐mounted module are used. For this reason, the accuracy of the measurement of the angle between the axis of rotation of a collimator and a local vertical direction must depend on the design of the table‐mounted module, in particular on its size and the number of markers. For almost minimal set of markers and a bigger phantom modules, it is possible to reduce the error α to approximately 0.02 degrees for clinical settings and 25 collimator angles used in a testing procedure.It is important to assess how the design of the testing procedure and the design of the phantom influence the accuracy of a measurement of geometrical parameters. The accuracy of a measurement of the angle between the axis of rotation of a collimator and a local vertical direction increases with increasing the number of collimator angles included in the testing procedure, the number of markers within the phantom modules and with phantom size. By increasing the number of collimator angles from 9 to 25, the error θ between nominal and calculated axis of gantry rotation depends on the number of gantry angles used to estimate it. With 25 gantry angles error θ is approximately equal to 0.7°. Increasing number of gantry angles by a factor of two decreases error θ by the same factor. With such a trend it follows that probing gantry angles at an interval of 1 degree, the error of estimation of the gantry rotation axis corresponds to about 1.5 mm deviation at 2 m distance from the isocenter.The accuracy of a measurement of the deviation ω between the estimated and nominal angle formed by the edges of a radiation field in an isocentric plane depends weakly on the number of gantry angles and the number of balls within the table‐mounted module. It is an indirect dependence as the contours of a radiation field are determined for a plane containing the isocenter and the accuracy in determining isocenter depends on the number of gantry angles. The measurement error ω depends more strongly on phantom size. With bigger phantom modules the error of a measurement ω can be reduced to 0.2° that correspond to 0.35 mm (one pixel) for a 10 cm × 10 cm radiation field.The value of the angular difference L between estimated and nominal lengths of the edges of a radiation field in an isocentric plane depend on the same components of the testing procedure as ω. With the bigger phantom design, the error of a measurement L can be reduced to 0.5 mm which is slightly larger than an EPID pixel.The values of differences s of the isocenter position in space depend on all components of the testing plan and on the phantom design. Increasing the number of gantry and collimator angles, the number of ball markers and the phantom size decreases the error s to different extents. It, however, follows that even for not very complex testing plans it is possible to reduce the error s to a submillimeter range.The values of the components SAD and SDD on the testing plan and the phantom design is the same. The errors of both SAD and SDD are independent of the number of collimator and gantry angles and on the number of balls in a collimator‐mounted module. This follows directly from the method of applying the phantom for estimating the geometrical parametersSDD, the error of SAD is of the order of 0.8 cm. Better estimation of SAD or SDD requires averaging over multiple measurements instead of using the result of a single measurement. If one averages values of SAD over, for example, 100 collimator angles (these kind of data must be collected anyway to find the rotation axis of a collimator), then the error of estimation of an averaged SAD decreases to submillimeter accuracy.The pattern of the dependence of the measurement error of It follows from the presented results that even when the resolution of an EPID is limited, it is still possible to perform geometric testing with satisfactory accuracy by proper selection of an architecture of the phantom and a testing plan. The presented results may provide guidelines for selection of a testing plan to achieve the submillimeter and subdegree accuracy of geometric testing procedures used in quality control in radiotherapy.4.1MQ to the nominal value NQ of a parameter Q. For this reason one is, in practice, interested in how big the absolute value of the difference between MQ and NQ is. Thus, to evaluate the results of a geometric test we have to calculate the probability Pr (|Q – NQ| = Δ ≥ ΔM = |MQ – N|Q):M) is the probability that in a device operating according to the assumed model  the observed difference between measured value of Q and a NQ is greater than ΔM. Clearly, if Pr(Δ ≥ ΔM) becomes too low, one may strongly conclude that the deviation of an actual device from the model is too serious and appropriate measures must be taken to correct it.The simulation tools developed in the present study and the results presented can be used in a future study to design a probabilistic framework for testing the geometry of a linac in a following way. The geometry testing usually involves comparison of TH and if Pr(Δ ≥ ΔM) is less than PrTH, then one concludes that the geometrical test has failed because for the used testing plan PT the probability of observing an actual difference ΔM in a correctly tuned device is lower than an accepted threshold PrTH. Equivalently, one may define a tolerated difference ΔTH by:M is larger than ΔTH. The distribution functions and probabilities can be derived directly from the simulation results, as demonstrated in the previous section.Then, to apply a geometry testing procedure, one may select a probability threshold PrTP can be stated and answered in a future study. First, assume that the value of a tolerated difference ΔTH must be respected due to some factors of clinical relevance. If a testing plan TP is not properly designed, the measured differences ΔM can be larger than ΔTH in substantial percentage of cases of correctly tuned devices due to purely random factors. Thus one may ask what must be the testing plan t,TP if it is required that the assumed value of ΔTH corresponds to some user‐specified probability threshold PrTH. In other words, both PrTH and ΔTH are given and only procedures t,TP such thatWithin the probabilistic framework described above questions about a testing plan, Q1 and Q2 are estimated resulting in measured values Q1,M and Q2,M, while the nominal values for Q1 and Q2 are Q1,N and Q2,N. We are interested in how the discrepancies Δ1,M = |Q1,M–Q1,N| and Δ2,M = |Q2,M–Q2,N| are correlated. In particular, for measurement discrepancies that are not independent it is possible that observing some specific pair of Q1,M and Q2,M is an unlikely event but such conclusion cannot be drawn from the analysis of the distributions of Q1 and Q2 separately. In this analysis, the random variable QJ =  with joint probability density function fQJ must be considered.The final problem that may be also addressed in future within a probabilistic testing framework is the independence of measurements of various parameters. In particular, assume that two geometrical parameters, say TH, the geometrical testing procedure may be complemented by a requirement that if an expected value of the geometric parameter differs from the nominal value by more than some acceptance threshold ΔTH, then such an event must be detected with a probability PowTH. Now, if the testing procedure must meet constraints about both PrTH and PowTH, the problem is how to select an appropriate testing plan TP to address these requirements. While the answer to this question is certainly important, it would require simulation of possible mechanical failures of a linac, for example to estimate the distribution of a geometrical quantity of interest in both correctly tuned and malfunctioning devices . Our simulation does not address such cases because modeling failures of a linac are not possible without detailed knowledge of its mechanical design.In the context of geometrical testing, another important problem can be formulated. Assume that the decision that a device passes or fails some geometrical test involving measurement of some geometrical parameter is made based on a preselected threshold probability Pr5In this paper, a new simulation‐based method for assessing accuracy of geometric tests of a linac is proposed and evaluated on a set of testing procedures. Parameters describing geometry of a linac are reconstructed from the projections of the centers of fiducial balls of a two‐module phantom after adding random errors to the coordinates of these projections. Assuming realistic accuracy of EPID image analysis it is shown that for selected testing plans the reconstruction accuracy of geometric parameters can be significantly better than commonly used action thresholds for these parameters. Proposed solution has the potential to improve geometric testing design.The authors have no relevant conflicts of interest to disclose.Data S1. Reconstruction procedures.Click here for additional data file.


A new way to control individual molecules and monoatomic chains is devised by preparing a human–machine augmented system in which the operator and the machine are connected by a real-time simulation. Here, a 3D motion control system is integrated with an ultra-high vacuum (UHV) low-temperature scanning tunnelling microscope (STM). Moreover, we coupled a real-time molecular dynamics (MD) simulation to the motion control system that provides a continuous visual feedback to the operator during atomic manipulation. This allows the operator to become a part of the experiment and to make any adaptable tip trajectory that could be useful for atomic manipulation in three dimensions. The strength of this system is demonstrated by preparing and lifting a monoatomic chain of gold atoms from a Au(111) surface in a well-controlled manner. We have demonstrated the existence of Fabry–Pérot-type electronic oscillations in such a monoatomic chain of gold atoms and determined its phase, which was difficult to ascertain previously. We also show here a new geometric procedure to infer the adatom positions and therefore information about the substrate atoms, which are not easily visible on clean metallic surfaces such as gold. This method enables a new controlled atom manipulation technique, which we will refer to as point contact pushing (PCP) technique. It is of fundamental interest both for chemists and physicists to study the electronic transport through single atoms and molecules. Scanning tunnelling microscopy bestows us with the capability not only to image single atoms and molecules when they are deposited on a conducting surface but also to study electronic transport through these entities –2. HowevThe system that we have developed addresses this problem. We have added a 3D motion control system to our STM that helps in making any required tip trajectory and combined it with a molecular dynamics (MD) simulator that simulates in real-time the manipulation process going on in the STM. The MD simulation not only provides information about the atomic scale structure of the junction, but also serves as a visual feedback to the operator in real-time who can then choose to make a desired trajectory for better control of the manipulation process. This is especially important in the case of 3D manipulation of single molecules and atomic chains, as there are no predefined accurate trajectories –6 that o−10 mbar pressure and most of the experiments were performed at 3 K temperature (the base temperature of 300 mK was not required). A custom-built 3D motion-control system running under LabVIEW is used to control the STM tip in all three dimensions during manipulation. x–y-motion and y–z-motion of the LED respectively. The LED is attached on top of the operator hand, such that the trajectory can be “drawn” by the operator hand and tracked by two cameras [x,y,z-signals with proper scaling factors before sending it to the STM tip and the simulation. The scaling factor converts approximately 10 cm of hand movement to 2 Å displacement of the STM tip. The usual imaging in STM is done using a commercial RHK SPM100 ver.8E controller. A mono-crystalline gold sample cut along the (111) surface is prepared by repeated argon sputtering and annealing cycles to obtain an atomically flat Au(111) facet showing herringbone surface reconstruction. We further prepare the surface at low temperature by creating a localized stress pattern [,  and ) as shown in The experimental setup used here is a custom-built cryogenic STM head  that is  cameras . Then, along the 1 surface pattern  on the sx,y,z- signals to both the STM and the simulator simultaneously and therefore the MD simulation is required to have a minimal time delay in its response for smooth real-time operation. By ‘real time’ we mean that the system in the simulation converges to a local energy minimum (an equilibrium position) between each subsequent probe position. The probe speed is determined by the operator, and depends on the speed with which the 3D motion control sensor is moved. In the scale of the operator this is approximately 5 cm/sec, which corresponds to 1 Å/sec on the atomic scale.A conventional atomic manipulation operation using STM involves a pre-defined trajectory (controlled by the operator or by an automated procedure) of the STM tip. An example is reducing the tip–sample distance and moving the tip in a desired direction assuming an isotropic nature of adsorption bonds  in metalWe perform a classical MD simulation here in which we ignore the electronic effects (which in fact give rise to interatomic forces) and take the forces as coming from parameterised equations that only depend on the interatomic distances. This is typically called a force-field simulation. A more accurate method would be obtained by using ab initio calculations that take into account both the nuclear and the electronic degrees of freedom. But these ab initio calculations are computationally very expensive and thus are not suitable for our purpose. The simulation we discuss in this article is only made for metallic systems, so in this case all the atoms involved are Au atoms. Here a semi-empirical potential described by Tománek et al.  and Cortrij is the distance between two atoms i and j, r0 is the equilibrium distance, and ζ, q, A and p are parameters that can be determined by fitting bulk material properties to experimental values. The parameters used for the results shown in this manuscript are: r0 = 2.884 Å, ζ = 1.8184 eV, A = 0.20967 eV, q = 4.03 eV and p = 10.145 eV. The energy of where a is therefore given by , another one to calculate energy and forces, and to integrate the equations of motion, and a third separate class to visualize the atoms.The molecular dynamics simulation is written in C++ to guarantee high computational performance. A schematic flowchart of the simulation execution is given in T0 with an adjustable coupling to a heat bath:We differentiate between three types of gold atoms, corresponding to the role they play in the simulation. In B is the temperature relaxation time, related to the strength of the coupling. The velocities of all atoms are rescaled at every timestep (Δt) with the same factor:where τB in condensed systems is of the order of 0.1 ps [A typical value for τf 0.1 ps . In our f 0.1 ps . In orderij, the distance between two evaluated atoms, is larger than the cutoff radius, the respective pair of atoms will not be taken into account in the energy and force calculations. Because of the exponential decay with distance in the potential, their contribution is very small. Moreover, as described in the book by Andrew Leach [Several optimizations and approximations are implemented to speed up the computation so that the simulation can run in real time. First, we introduce a cutoff radius of 7 Å in the calculation of forces and energy between pairs of atoms. The exponential functions from ew Leach , just us−4 percent . The larger distances are updated less frequently, only once every 50 simulation steps. Secondly, we implement a lookup table to increase the calculation speed of the exponential functions that still need to be found. This means that the exponential function is evaluated for a long list of relevant interatomic distances at the initialization of the simulation. Every time it needs to be calculated during runtime, a linear interpolation of the precalculated values around the given distance is used instead of calculating the exponential itself. Looking up the value from the lookup table is faster than calculating it, resulting in better performance. We have compared this speed up in simulation due to the aforementioned approximations with a standard implementation of the MD simulations without any approximations. For this we performed a structural relaxation step in a system analogous to the one shown in A supporting program has also been developed to setup a simulation stage based on the STM images taken during the experiment prior to the start of the main program. To prepare an exact stage as in the experiments, it requires not only the exact knowledge of the positions of adatoms on the surface but also the atomic configuration of the surface and the STM tip. The atomic shape of the tip is always an unknown quantity in STM. One could obtain partial information before the start of the experiment using field ion microscopy (FIM), but after a few manipulations steps the tip shape would become unknown. We developed a localized tip-shaping procedure published elsewhere , which hIn this section we will show how the above system with the real-time MD simulation works using some simple lateral manipulation test followed by an experiment where we lifted a chain of Au atoms out of the surface in a controlled manner forming a free-standing atomic chain between the tip and the sample. Some challenges in creating such a free-standing atomic chain using a controlled STM technique are addressed by Tartaglini and co-workers . These aAnother interesting phenomenon from the electronic point of view that was also found experimentally  was that or atomically sharp step edges and the location of FCC or HCP packing. The atomic orientation and packing of metallic Au(111) surfaces is not readily available from STM images (see Standard STM images of the Au(111) surface can provide the information about the crystallographic directions from the herringbone reconstruction  surface each time. The method is not limited to the Au(111) surface. A similar geometrical argument can be used on other surfaces as well, and it can be used to determine, e.g., on-top, bridge, and hollow adsorption sites of small molecules. A related approach by tracking an adatom movement and position to get the information about the background lattice has been reported earlier by Böhringer and co-workers . After hWe start now our experiment in the configuration shown in We have performed manipulation in a new point contact pushing (PCP) mode with feedback loop switched off. The difference between our PCP mode and the common lateral manipulation mode is that we do not move the tip in a straight path but we move from hollow site to hollow site by bringing the tip always in-line with the path to the next hollow site and then push the adatom. This is done so that the adatom position can be known and controlled at each step of the manipulation and avoids the complex jumps and movement of the adatom depending on the relative alignment of the underlying lattice and the manipulation direction . AnotherG0 conductance. This is different from some previous works that have shown that a jump to contact occurs only when approaching a bare metallic surface, while when approaching an adatom on the surface there is a smooth transition from tunnelling to contact [Z constant. Similar to the jump to contact phenomenon that happens while approaching a surface or an adatom from the top, a jump to contact also occurs while approaching the adatom laterally parallel to the surface. Because the corrugation energy in metallic surfaces is usually 1/10 to 1/3 of the adsorption energy [In our manipulation method we first match the tip height in the simulation with respect to the experiment by going above an adatom in point contact in the experiment resulting in a jump to contact and a stable level at 1 contact ,40. This contact  that the contact  of tip a contact –44, alben energy , this jux,y,z-curves and x,y,G-curves for this operation are given in Being thus prepared we used the PCP method to first move the adatom ‘A’ shown in Successful demonstration of manipulation using our PCP technique sets a boundary of validity of our real-time simulation. However, demonstration of the controlled lift-off of a chain of gold atoms above the Au(111) surface would depend on many different parameters that could affect the interatomic forces and are not included in simple semi-empirical potentials used here. Such parameters comprise the atomic shape of the actual tip apex in the experiment, which defines the depth of the potential well on the tip in comparison to that on the surface, and moreover the inelastic excitation of vibration modes of the adatom –47 due tZ-coordinate variation over time. The corresponding x,y,G-graph for this operation is given in Z constant) in feedback-off state towards the adatom. Next, a lateral jump to contact happens, which gives a sudden change in conductance to approximately 1G0, as can be seen from point 5 to 5’ in In the second step, we start now from position ‘ii’ and move the adatom ‘A’ to position ‘iii’ and then continue with the operation of lifting-off the atomic chain followed by taking an STM image at the end . Figure Z-position in Z-value of 0.45 nm, and adding to this 0.12 nm (which is the Z = 0 point given by the tip height from surface during pushing) gives 0.57 nm, which is very close to twice the covalent diameter [Then the adatom is moved towards the other pair of atoms ‘B’ and ‘C’ to position ‘iii’ going from one hollow site to the next hollow site (‘L’ to ‘R’ or ‘R’ to ‘L’) shown as the meandering part in diameter  of a sinThe conductance of a macroscopic conductor decreases with increase in its length. But in small atomic-scale conductors, due to the ballistic nature of electronic transport, the conductance should not change with the length of the conductor. However, chain-length dependent oscillations in the conductance in monoatomic chains have been reported by the name of parity oscillations or even–odd oscillations. In experiments with gold atomic chains, such parity oscillations are demonstrated by making length histograms using a MCBJ setup ,49–50. TThe controlled experiment described in Eventually, when attempting to pull the tip further expecting the adatom ‘C’ to join in the chain, the chain broke. The STM image taken at the end  shows twWe have modified our low-temperature ultra-high vacuum STM with the integration of a 3D motion control system and a real-time molecular dynamic simulation. This human–machine augmented system where the operator can become part of the experiment and make adaptable STM tip trajectories based on the visual feedback from simulation, provides a better control for (3D) atomic manipulation. This method should become particularly useful for molecular manipulation. Furthermore, we demonstrated how a simple geometric technique based on placing two adatoms can give information about the atomic configuration of the metallic substrate. We used this as the input to setup the same environment in the coupled real-time simulation and demonstrated the controlled lift-off of an atomic chain. For this purpose, we developed a new point contact pushing technique that can directly be followed by the manipulation into the third dimension at the end. By placing this atomic chain back and forth between freely suspended and surface resting position we studied the parity oscillation behaviour in conductance, which occurs due to interference of electronic waves in different length of the chain. For a better comparison with theory and a possible direct feedback loop from the experimental conductance values, a real-time conductance estimation based on the atomistic positions given by the MD simulations could be useful. Tight-binding models have been known  to give Supporting Information includes derivation of the force expression given in the main text. A schematic flowchart of the simulation execution is also provided. A detailed discussion about the geometric method for determining the positions of the background substrate atoms is given as well. The plot showing the effect of using the cut-off radii and look-up tables in the simulation is also provided. Conductance and trajectory data recorded during experiments are shown as 3D plots. A full sequence of the manipulation shown in the simulation is also available as a video file.File 1Additional data.File 2Simulation step 1.File 3Simulation step 2.


W boson, The results of a search for new heavy  W and Z bosons and are generically referred to as W boson. This model represents a good benchmark as the results can be interpreted in the context of other models of new physics, and is useful for comparing the sensitivity of different experiments.Extensions to the Standard Model (SM) may include heavy gauge bosons that could be discovered at the Large Hadron Collider (LHC) . For exael (SSM)  posits alepton , with respect to a sample of loose lepton candidates in a background-enriched sample. These loosely selected candidates satisfy only a subset of the nominal criteria, which is stricter than the trigger requirements imposed. Potential contamination of prompt final-state leptons in the background-enriched sample is accounted for using MC simulation. In addition, the fraction r of real leptons in the sample of loose candidates satisfying the nominal requirements is used. This fraction is computed from MC simulation. The number of jets and photons misidentified as leptons  observed in the data is about 23. The effect of pile-up is modelled by overlaying simulated inelastic pp collision events selected using very loose trigger requirements (“minimum bias”). All MC samples are reweighted so that the distribution of the number of collisions per bunch crossing matches the data. Correction factors to account for differences observed in the detector response between data and simulation are applied to the lepton trigger, reconstruction, identification [The MC samples were processed through a simulation of the detector geometry and response  using thGeant4  frameworfication , 27 and fication .The analysis makes use of electrons, muons, and missing transverse momentum, whose reconstruction and identification are explained in the following.loose, medium and tight working points are defined. Full details of the electron reconstruction, identification and selection working points can be found in Ref. [Electrons are reconstructed from ID tracks that are matched to energy clusters in the electromagnetic calorimeter obtained using a sliding-window algorithm in the range  in Ref. .Muon candidates are identified from MS tracks that match tracks in the ID, with |η|<2.5  . These mz-position of the point of closest approach of the muon track in the ID to the beamline and the z-coordinate of the primary vertex, must fulfil The ID tracks associated with electron and muon candidates are required to be consistent with originating from the primary interaction vertex, which is defined as the vertex whose constituent tracks have the highest sum of The missing transverse momentum is reconstructed as the negative vectorial sum of the calibrated momenta of electrons, muons and jets, where the electrons and muons are required to satisfy the selection criteria described above . The jetclusters  in the clgorithm  with a rlgorithm  and are medium identification criteria, or at least one electron with loose identification criteria. The identification criteria for electrons at trigger level are similar to those used in the offline reconstruction [Events in the muon channel were recorded by a trigger requiring that at least one muon with truction .tight identification criteria, and the electron medium identification criteria or muons with Events recorded by the trigger are further selected by requiring that they contain exactly one lepton. In the muon channel, the magnitude of The expected number of background events is calculated as the sum of the data-driven and simulated background estimates described in Sect. mentclass2pt{minimmentclass2pt{minimmentclass2pt{minimmentclass2pt{minimThe systematic uncertainties arise from experimental and theoretical sources. They are summarised in Table Experimental systematic uncertainties arise from the trigger, reconstruction, identification and isolation efficiencies for leptons , 27, andZ boson candidates found in data. The ratio of the efficiency measured in data to that of the MC simulation is then used to correct the MC prediction [tight identification working point. This uncertainty is based on the differences observed in the electron shower shapes in the EM calorimeters between data and MC simulation around the The electron and muon offline reconstruction, identification and isolation efficiencies, and their respective uncertainties, are assessed up to ediction , 27. For in Ref. , which rThe main systematic uncertainties in tainties  and the tainties . The uncW and Theoretical uncertainties are related to the production cross-sections estimated from MC simulation. The effects when propagated to the total background estimate are significant for W and VRAP to calculate the NNLO cross-section as a function of the boson mass. Rather than using the original 28 CT14 uncertainty eigenvectors, a re-diagonalised set of seven PDF eigenvectors, as provided by the authors of the CT14 PDF using MP4LHC [Theoretical uncertainties in the g MP4LHC , 35, is entclass1pt{minimag MP4LHC  and NNPDg MP4LHC  PDF setsUncertainties in the electroweak corrections are determined as the difference between the additive approach  channel includes a 15% (100%) normalisation uncertainty. This uncertainty is dominated by the dependence of the factor For the The modelling of the pile-up especially affects the calculation of x–y beam-separation scans performed in August 2015 and May 2016.The uncertainty in the combined 2015 and 2016 integrated luminosity is 3.2%. Following a methodology similar to that detailed in Ref. , it is dFor the statistical analysis of the results presented in this section, the same methodology is applied as in the previous ATLAS mentclass2pt{minimmentclass2pt{minime effect  is takenBased on the above findings, upper limits on the cross-section for producing a analysis  with a uW boson production. The observed (expected) lower mass limit for a The 95% CL upper limits on entclass1pt{minimaentclass1pt{minimapp collision data recorded by the ATLAS detector at the Large Hadron Collider in 2015 and 2016. Examining the transverse mass spectrum, no significant excess above the expected Standard Model background is observed. Exclusion limits at 95% CL are placed on the mass of benchmark Sequential Standard Model The results of a search for a new heavy gauge boson decaying to final states with a high-


Surface soil structure is very responsive to natural and anthropogenic impacts and these changes alter soil hydraulic properties and the soil water budget. In the midst of a dearth of efforts to capture soil structural dynamics, an analytical solution to the Fokker-Planck Equation with physically-based coefficients has shown promising results in predicting the evolution of soil pore space in agricultural soils. In this study, the Python code for the analytical solution is shown along with steps to estimate coefficients leading towards obtaining the analytical solution.•Python code for modeling the evolution of soil pore space based on an existing model is shared.•The code for the estimation of physically-based coefficients of the model and parameter optimization are also shown.•The final output of the model may be used in estimation of soil water retention and hydraulic conductivity functions. Specification Tabler) ≥ 5 μm is expected to be the most affected by management practices such as tillage and natural stresses . The need for inclusion of soil pore dynamics in hydrological models to improve their reliability and accuracy has been stressed in recent times  is the total initial porosity, rm [L] is the initial median pore radius or geometric mean and σ [-] is the standard deviation of the log-transformed pore radius. Leij et al. [5] assumed ϕ0 to be the difference between saturated and residual water contents: ϕ0 = θs – θr. Finally, rm is calculated from the Young-Laplace equation where r = A/h, where A is a proportionality constant obtained from the variables of the equation, A = −0.149 cm2 and h [L] is the pressure head. The code for the initial PSD is shown in Eq. n) are calculated through division by the zero-order moment (m0). The code to obtain the zero order moment is shown in The coefficients of the PDE are calculated following the approach of  who used0m values to check if the probability was preserved. If the probability was not preserved, we included the degradation term in the analytical solution. The code for the degradation term is shown in The degradation term is expressed by means of an exponentially decaying function :(8)Mt=d×1 characterizes the mean pore size 〈r〉 [L]:The first-order normalized moment MThe first-order moment can also be obtained from other independent models . For insThe code for both these scenarios are shown in 2 characterizes the variance [Finally, the second-order centralized moment μvariance :(11)μ2=rλ.λ is obtained by fitting Eq. However, our lack of knowledge on how the dispersion behaves with respect to the pore size paved the way to use the dispersivity As a final step, the pore size distribution  is obtained using the code in The optimized lambda value should now be used in the code a and b iThe possibility of using other independent models for the coefficients exists and is being looked into. Further, the optimization process for lambda necessitates the final water retention parameter values making the model redundant. However, lack of sufficient data sets that capture the temporal dynamics of soil structure hampers our quest to establish a range of values for the coefficients as well as for the validation process. In conclusion, the model is able to capture very well the evolution of soil pore size distribution in its current state with scope for improvement in how we estimate the coefficients.


There is a large number of people that have knee degeneration in China. Total knee arthroplasty is one of the most effective methods of treatment in the later stages of the disease. However, there are challenges when performing total knee arthroplasty on patients with ipsilateral hip akylosis. So far, there are few reports on postoperative curative effect of total knee arthroplasty for these patients. This case report records how to perform total knee arthroplasty in a patient with ipsilateral hip ankylosis.Due to ankylosing spondylitis, the flexion of the patient's hips are restricted in 10°, which leads to a limited ipsilateral knee flexion to 30° when she is in the supine position.Right knee osteoarthritis; right hip ankylosis.We modified the traditional surgical position to allow easy exposure of the knee during surgery. After total knee arthroplasty, the patient was included in a planned training program, and was followed for 6 months.The patient walked well without ambulation aid and achieved satisfactory knee joint function.Conversion of a fused hip to a total hip arthroplasty does improve the quality of life of patients, but, given the high incidence of complications and more financial burden to the patient, we modified traditional surgical position of the patient to provide ideal surgical exposure of the knee. We hope that this case can be used as a reference for clinicians to deal with similar situations. The treatment challenges for total knee arthroplasty combined with hip ankylosis is how to solve the problem of limited knee movement during surgery. So far, there are few reports about the total knee arthroplasty in a patient with ipsilateral hip ankylosis and the postoperative curative effect. Our case report records how to conduct total knee arthroplasty in a patient with ipsilateral hip ankylosis who had ipsilateral hip fused in 10° of flexion and restricted knee flexion at 0° to 30°.Total knee replacement is considered one of the most cost-effective treatments for final stage knee osteoarthritis to relieve pain and recover joint function.2Our patient is a-64-year old Chinese female with knee pain of more than 10 years and limited activity for 7 years. The purpose of admission is to perform the right knee replacement to relieve pain and restore joint function. The patient suffered from chronic suppurative arthritis and chronic osteomyelitis caused by the right hip injury about 50 years ago, and she is currently suffering from right hip ankylosis. Eight years ago, she was treated with reduction and internal fixation of lumbar spondylolisthesis. The patient can walk independently without help, but is limited to 100 m due to knee pain. Many of her basic life activities cannot be completed, including wearing socks.Physical examination: Right hip has sinus closure scar and hip joint fused in 15° of abduction, 15° of flexion, and 20° of external rotation and ipsilateral knee joint fused in 20° of flexion. There was tenderness in the medial joint space of the right knee and a sense of friction during activity. The patella grinding test was positive and patella lateral movement was less than 0.5 cm. Right knee range of motion was within 20° to 90° and friction fremitus was felt in the activity. Her right lower limb is 2 cm shorter than the left leg.Preoperative radiographs: Her preoperative radiographs are as follows. Figure  the patients was include in a rehabilitation plan focusing on range of motion of the knee after surgery.Methods : Knee arthroplasty with ipsilateral hip fusion faces difficulty in exposing the knee joint in the traditional supine position. In the supine position, the patient's hip joint is fixed at 15° of flexion, while the ipsilateral knee has a maximum flexion of only about 30° Fig. . Figure Outcomes and follow-up: The total follow-up period was 6 months. The patient was in good condition after surgery, and can walk with the help of ambulation aid on the 2nd postoperative day. Two weeks postoperatively, her right knee range of motion was at 0° to 90° (Fig. 3,7 They conclude that performing total knee arthroplasty alone in patients with an ipsilateral fused hip ended in unsatisfactory results. However, their conclusion might be contributed into a lack of data. Conversion of a fused hip to a total hip arthroplasty does improve the quality of life of patients; however, a number of retrospective studies have shown that the conversion of hip arthrodesis to arthroplasty increases the risk of nerve injury and heterotopic ossification. Considering the possibility of a higher rate of complications in this specific situation, many data indicate that performing total hip arthroplasty is controversial, and may not be necessary if hip had been fused at an acceptable position.–10For total knee arthroplasty candidates who have ipsilateral hip arthrodesis, Romness et al and Rittmeister et al suggest the fused hip need to be made into a mobile joint before surgery. They changed the traditional supine position to allowed the knee to flex up to 100° on the operating table which originally can only flex up to 70° by elevating the fused hip joint. Goodman et al presented a different kind of body position to address the problem of exposure, especially in patients with the stiffness of the arthritic knee. By adjusting the height of the table tail episodically, they can change the flexion angle of the knee joint to achieve precise positioning and osteotomy. Comparing to Goodman et al's plan, Koo et al's plan had lager knee range of motion in the operation. While considering the effect of the stiffness of the arthritic knee, Goodman et al's approach has a more widely application. However, neither plan mentioned the placement of the contralateral lower limb.The technical challenge of knee arthroplasty for patients with ipsilateral hip fusion is how to solve the problem of limited knee movement during surgery. Koo et al wrote a case report and proposed a solution to overcome the challenge in the knee replacement in a patient with existing ipsilateral hip fusion.How to solve the restriction of knee joint activity in operation is a technical problem when performing total knee arthroplasty in a patient with an ipsilateral fused hip. Conversion of a fused hip to a total hip arthroplasty does improve the quality of life of patients, but it accompany with high incidence of complications and more financial burden. We modified the patient position to facilitate operation process. However, the limitation of this study is that there is only 1 case and the follow-up time is not long enough. We hope that this case can be used as a reference for clinicians to deal with similar situations.The authors would like to thank this participating patient, as well as the study nurses, co-investigators, and colleagues who made this report possible.Conceptualization: Wanchun Wang, Tang Liu.Resources: ZuYun Yan.Writing – original draft: XianZhe Tang, ZuYun Yan.Writing – review and editing: Tang Liu.


It was found that the por-Si template causes a negative surface potential of silver particles and their chemical resistivity to oxidation. These properties provided to attract positively charged lactoferrin molecules and prevent their interaction with metallic particles upon 473 nm laser excitation. The SERS spectra of lactoferrin adsorbed from 10−6 M solution were rather weak but a decrease of the concentration to 10−10 M led to an enormous growth of the SERS signal. This effect took place as oligomers of lactoferrin were broken down to monomeric units while its concentration was reduced. Oligomers are too large for a uniform overlap with electromagnetic field from silver particles. They cannot provide an intensive SERS signal from the top part of the molecules in contrast to monomers that can be completely covered by the electromagnetic field. The SERS spectra of lactoferrin at the 10−14 and 10−16 M concentrations were less intensive and started to change due to increasing contribution from the laser burned molecules. To prevent overheating the analyte molecules on the silvered por-Si were protected with graphene, which allowed the detection of lactoferrin adsorbed from the 10−18 M solution.We registered surface enhanced Raman scattering (SERS) spectra of the human lactoferrin molecules adsorbed on a silvered porous silicon ( However, there is an effective way to solve this problem via the placement of analyte molecules on a surface of nanostructures of coinage metals that provides a great enhancement of the Raman signal by several orders of magnitude por-Si anpor-Si. −6 to 10−18 M concentrations, which were obtained by the collection and integration of the SERS spectra maps. We used two SERS-active substrates from different batches and scanned a 10 × 10 μm surface area of both substrates with a step of 1 μm. Each point of the maps was excited for 2 s. The laser power was decreased to 0.14 mW in contrast to the previous measurement to eliminate a harmful photothermal effect.Next, we revealed the minimal concentration of the lactoferrin solution at which its molecules are still detected after adsorption on the silvered −6 M is rather weak but the decrease of the concentration down to 10−12 M led to the enormous growth of the SERS signal. Lactoferrin mostly exists in tetramer and monomer forms [−10 M while the lower amount of this analyte leads it to turning into a monomer form. Tetramers are too large for the uniform interaction with the electromagnetic field from the silver particles to provide an intensive SERS signal from the top part of the molecules. At the same time, monomers can lay between the metallic structures and be completely excited. The SERS spectra at the 10−14 and 10−16 M concentrations have lower intensities and at 10−18 M the pattern typical for amorphous carbon is observed.The SERS spectrum of lactoferrin adsorbed from 10er forms ,66. Supp−1) become broader. We still observe bands at 1002–1005 cm−1 (Phe ring breathing mode), 1130 cm−1 (corresponding to C-N bonds), 1350 and 1380–1390 cm−1 (Trp residues), 1450 cm−1 (δCH2), 1610–1615 cm−1 (Tyr) and 1647–1650 cm−1 (Amide I). The bands at 859 cm−1 (the asymmetric C-C-S stretching of Met side) and at 1170 cm−1 (the CO bending of the phenolate ligand) are now prominent in contrast to the previous single measurement due to a better enhancement and spectra integration. We also see intensive Tyr bands at 1257–1260 and 1290 cm−1. Alternatively, one of these bands can be Amide III and signify the domination of the α-helical structure, which is also proved by the position of the Amide I band. In this case, the Amide I band related to the beta strands is hidden in more intensive bands of alpha helices. Therefore, the signature of only β-sheet structure in the spectrum registered for the higher laser power could be caused by overheating. Unfortunately, the bands at 1547 and 1560 cm−1 can be overlapped by the wide band of amorphous carbon with maxima at 1576 cm−1. However, the spectra analysis gives an idea that this doublet coalesced in one band shifted to 1560 cm−1 because no hint of any band at 1547 cm−1 can be found. If so, this can confirm that the prevalent orientation of the indole ring is at an intermediate angle.All the informative SERS spectra are characterized by the presence of this analyte bands. Some burning of the analyte with the concentration decrease is observed as bands related to the amorphous carbon  for 10−6 and 10−12 M concentrations are presented in −10 M led to the accumulation of the lactoferrin molecules in the nanoparticles (precipitations) with diameters of a couple to a hundred nanometers. The use of the more diluted solutions resulted in the accumulations size smaller than two nanometers or no accumulations at all.For the deeper understanding of the adsorption of the lactoferrin molecules on the SERS-active surface they were studied by SEM and EDX after immersion to the lactoferrin solutions at different concentrations. It was revealed that at the 10nometers a,b. The ulations c,d. Supp.132 nm3  and we cpor-Si down to the 10−16 M concentration. However, at the 10−18 M concentration we found just the bands corresponded to the amorphous carbon. We suppose that the 10−16 M concentration is still enough to provide adsorption a plenty of molecules at several close to each other silver particles, which are in the laser spot. This allows getting the enhanced signal from a number of molecules located around the central point in the laser spot that is the most heated. Lower concentration leads to less amount of the adsorbed molecules, which cannot provide getting of proper enhancement within the laser spot, while burned species result in the high interference from vibration of amorphous carbon bonds.We were able to analyze the lactroferrin molecules adsorbed on the silvered −1 were used . Therefore, to objectively estimate the lactoferrin concentration it is recommended to measure the SERS intensities of two or even more bands.Usually an analyte concentration during the SERS measurements is estimated using a comparison of intensities of the selected bands reflected in a calibration curve. As a rule, the intensity of the signal decreases with the concentration lowering. This dependence results in a linear calibration curve. The data obtained in our work do not have an ordinary view, i.e., the SERS signal intensity of the analyte is not directly correlated with its concentration. This is caused by the specificity of adsorption and the distribution of the lactoferrin molecules and their structural form at different concentrations. Therefore, the calibration curves have a non-linear character. The intensities of the bands at 1005 and 1290 cmere used  to find −16 M lactoferrin concentration, at which it can be detected, we used the protection with graphene that was tested on the R6G molecules in the −18 M concentration, there are 10−21 moles of the protein molecules. Multiplication of this amount by Avogadro’s constant will give 602 lactoferrin molecules. The SERS-active area was 0.25 cm2 (=25 × 106 μm2) so there are 25 × 104 square maps of 100 μm2 area on it. Even if all the molecules are adsorbed on the SERS-active surface, the probability to catch one lactoferrin molecule in one map is negligibly small and can be calculated as 602/(25 × 104) ≈ 0.24%. That is why we recorded several maps before the lactoferrin spectrum was found. It should be noted that the maps were chosen from the light areas of the sample surface, which contain 1–8 graphene layers. por-Si and then coated with graphene. We registered spectrum during 2 s. Despite the SERS spectrum intensity being relatively low, most of the lactoferrin Raman bands were presented there: 1002 cm−1 (Phe), 1290 cm−1 (Amide III), 1340 cm−1 (Trp), 1440 cm−1 (δCH2), 1605 cm−1 (Tyr) and 1642 cm−1 (Amide I).To overcome the limitation of the 10−16 M. To check the presence of the lactoferrin molecules the SERS-active substrate should be covered with the graphene-containing layer after immersion in the water solution. If the SERS mapping reveals the lactoferrin spectra, the concentration of the analyte will be 10−18 M.Therefore, if the graphene-free substrates result in non-informative SERS spectra this can signify that the analyte concentration is lower than 10Considering the non-uniform distribution of the lactoferrin molecules that have a tendency to get together on the substrates, it is reasonable to assume that a laser could hit the spot of several or even more molecules.por-Si and the graphene protection of the analyte molecules were applied. We were able to measure the SERS spectra of the human lactoferrin molecules adsorbed on the silvered por-Si from the 10−6–10−18 M water solutions. It was found that the por-Si causes a negative surface potential of silver particles and their chemical resistivity to oxidation in contrast to those deposited on the c-Si surface. It must be caused by an extremely developed surface of the por-Si template enriched with silicon broken bonds. These features promoted the attraction of the positively charged lactoferrin molecules and prevented their interaction with metallic particles upon 473 nm laser excitation, which typically is not used to study proteins. The SERS spectra of lactoferrin adsorbed from 10−6 M solution were rather weak but the decrease of the concentration down to the 10−10 M level led to the enormous growth of the SERS signal. This effect was observed because at the 10−6–10−8 M concentrations protein molecules coalesced in accumulations of its nanoparticles that are too large for the uniform interaction with the electromagnetic field from the silver particles to provide an intensive SERS signal from the molecules. Lower concentrations led to the adsorption of much smaller particles  that can be completely excited. Considering the tendency of lactoferrin oligomers breaking to the monomers while its concentration in solution decreases [−14 and 10−16 M concentrations were less intensive and started to change (more prominent amorphous carbon bands) due to heating to the temperature of lactoferrin denaturation at about 350 K. To decrease the temperature in the laser spot to 340 K, the analyte molecules on the silvered por-Si were protected with graphene, which allowed detecting lactoferrin adsorbed from the 10−18 M solution. All the registered SERS spectra of lactoferrin contained most of the vibrational bands typical for this analyte. Therefore, the SERS-active substrates based on the silvered por-Si can be used for the label-free study of the correlation of vibrational wavenumbers of protein and to find lactoferrin in its water solutions at the concentrations down to attomolar. It should be mentioned that according to our knowledge a reliable SERS study of the lactoferrin molecules adsorbed on the solid SERS-active substrates has not been reported before. However, we have not yet estimated the lactoferrin concentration in any mixture of proteins or in the biological fluids. This research is now undergoing to apply the SERS-spectroscopy with the substrates based on the silvered por-Si both free and protected with graphene to detect lactoferrin in complex proteins’ solutions and physiological fluids.In the present work, we overcame the hurdles of the SERS-spectroscopy to study the biomolecules with high molecular weight using the lactoferrin as test analyte. To achieve the objectives of the work, the SERS-active substrates based on the silvered ecreases , this re


Amantadine, a US FDA-approved antiviral drug, is a substrate for SSAT-1 and can be used to indirectly measure SSAT-1 activity because of its conversion to acetylamantadine (AA). This study was undertaken to further validate SSAT-1 activity in breast and lung cancer patients.Spermidine/spermine NAn increase in the urinary concentration of AA in lung and breast cancer patients was observed. The 0–2 h collection time point was determined to be optimal in revealing significant differences in urinary AA concentration between healthy controls and cancer patients.The high urine concentration of AA could be used as a simple and useful test for the detection of breast and lung cancer.  This study describes a novel noninvasive urine test for detecting and screening of breast and lung cancer using a safe and approved drug called amantadine. Higher concentration of the acetylated form of amantadine in the urine are detectable in the urine of both breast and lung cancer patients as compared with healthy adult volunteers. This test is simple and may serve as a useful tool for determining the presence of breast and lung cancer. Analyte recoveries from urine were stable in urine for 96 h at room temperature from and after up to three cycles of freeze/thaw in a range of pHs between 3 and 8 at 80 ng/ml. The LC–MS/MS assay method was successfully implemented for the measurement of AA in human urine collected from the present clinical study.Cross validation of findings was performed with HPLC of urine samples for the presence of AA ,17. SampFor the comparisons of the data presented in The mean age (± SEM) of the healthy control group at the Winnipeg site  was 38 ± 4 years, while the mean age (± SEM) of the healthy control group at the Bangladesh site  was 45 ± 3 years. Selected demographics of the participants with cancer in this study are shown in max  was 2 and 4 h in the fasted and fed state, respectively. There were no significant differences in the other pharmacokinetic parameters for amantadine disposition. Amantadine relative bioavailability was not affected by being in either fed or fasted state  and 8.20 , respectively.Analysis of the urine samples revealed that there was a higher concentration at 2 h of urinary AA in the lung cancer group as compared with healthy controls A. AlthouAnalysis of the lung cancer urinary AA concentration at the Winnipeg site revealed that a higher AA concentration was measured at both 2 and 4 h as compared with healthy adult controls A. AlthouWe have recently reported that human cancer is associated with high urinary concentration of AA . In the It should be pointed out that we did not observe any side effects with the single, one-time dose of amantadine ,20 in eiN-acetyltransferases (NATs), since amantadine is not a substrate for acetylation by either NAT1 or NAT2 [in vitro and in vivo studies in order to justify consideration of these substrates, other than amantadine, as suitable diagnostic tools for assessing upregulation of SSAT1.We have previously reported that amantadine is a specific substrate for SSAT-1 and can differentiate between acetylation by SSAT-1 and other  or NAT2 ,13. Thus or NAT2  and curr or NAT2 . FurtherIt is important to note that approximately 25% of the healthy adult controls  were deemed to be outliers with AA concentrations higher than expected. Accordingly, we have conducted a thorough examination of this group. At this point, a 6 and 9-month follow-up with the amantadine test has been conducted along with comprehensive clinical and hematological assessments. These findings are not in the scope of the present study, but are the focus of a subsequent paper. However, in this regard, it is interesting to note that we have previously observed regional/ethnic differences in AA concentration in healthy adults ; in ordeWhile current standards for determining and verifying the presence of cancer involve computed tomography (CT), MRI and ultrasound in conjunction with other molecular and protein biomarkers, they are expensive, often inaccessible, involve exposure to ionizing radiation and have an unacceptable level of false positives. In addition, biopsies for molecular and biomarker diagnosis are invasive and uncomfortable. Clearly, CT screening is capable of identifying early lung cancers. The issue of overdiagnosis is a limiting factor, generating anxiety for patients and adding expense for the healthcare system . The racin vitro anticancer activities [On the other hand, the polyamine pathway has been suggested to be an attractive target for the development of novel anticancer therapies . Indeed,tivities , and to tivities . Althougtivities ,39, theytivities . Therefotivities ,41. InhiThe amantadine acetylation test is a less expensive, noninvasive and simple to use tool with high clinical applicability and significance that can detect the presence of breast and lung cancer, while on the basis of our findings SSAT-1 may also serve as an important and novel therapeutic target for at least breast and lung cancer.Our earlier and present findings have provided evidence for the use of amantadine as a simple screening test for the detection of cancer as well as potentially a surveillance test in populations at high risk for developing cancer. It is also very possible that the test could be used for monitoring patients after surgical or chemo/radiation therapy to detect not only the response of the tumor to the intervention, but it could also have the possibility to detect the proliferation of new cancer cells. This is currently under investigation. It is also pointed out that we are in late development stage of including specific metabolites within the polyamine pathway metabolomic fingerprinting panel that will further the robustness of the assay performance. While the ROC curves presented in this study are for the single metabolite (AA), it is anticipated that inclusion of two or more metabolites within the polyamine pathway will increase AUC values further.Lung cancer is the leading cause of cancer death among both men and women.th as a leading cause of death globally and by 2040 is projected to rise to the 9th leading cause of death.Currently lung cancer ranks 13Breast cancer is the most common cancer in women worldwide.The utility of amantadine as an agent to demonstrate increased SSAT-1 activity linked to these cancers was performed.Higher urinary concentration level of AA is detectable in patients with different subtypes of lung cancer and breast cancer, which may also be related to staging.The detection of AA has the potential as a novel, simple-to-use test for the presence of lung and breast cancer.


Netherlands Heart Journal Mann et al. [In this edition of the n et al.  describeIn the current climate of scepticism relating to cell-based therapies as treatment for heart disease it is all too easy to accept this as another piece of evidence suggesting that the autologous cell-based therapy approach has failed after many years of small phase II clinical trials showing mixed results but no clear-cut overall efficacy signal. However before closing the door on this promising area of research (which provides a relatively cheap way of delivering cell-based therapies) we need to understand why others have shown beneficial effects of the autologous approach and whether further work is needed before reaching a definitive conclusion.It should be remembered that chronic heart failure represents an unmet need with regard to new therapies that can change symptomatic and prognostic outcome. The number of patients diagnosed with heart failure is increasing across Europe despite advances in pharmacological, device-related and pathway-specific changes to the management of heart failure. Heart transplantation continues at a low level across Europe and is not sufficiently available to treat this increasing burden of disease. Mechanical support devices have undergone substantial refinement but still provide a high cost option to the selected few.It is therefore important to carefully consider any new therapies that may help solve the heart failure burden as well as being ready to dismiss novel approaches following a rigorous programme of evaluation.Regarding the use of autologous cells for the treatment of heart failure the results of the metanalyses suggest a beneficial effect. However this has not been taken forward in the design of a definitive large trial to answer the question in the usual recognised approach. Instead small-scale trials with differing methodologies continue to be performed, adding to the confusion. Therefore there remains a need to ensure that clinical trials are performed with rigour and attention to detail. In the same way that the culturing of cells relies on meticulous attention to reagents and culture conditions, cell therapy in the clinic should be considered similarly. Previously the European Society of Cardiology Task Force for Stem Cells in Cardiac Disease published recommendations  regardinSo where does the trial reported by Mann et al.  fit? TheThus the rationale for intramyocardial delivery of autologous cell therapy for the treatment of heart failure is scientifically justified but not clinically proven. The trials that have been performed to date, including the work of Mann et al. , highligTaking all of this together the field of regenerative medicine as applied to the heart needs a rethink. Conceptually the ideas are solid. However the approach up until now has failed to live up to the high expectations of the cardiology community across Europe. New approaches to funding academic consortia are needed if we are to complete the scientific processes that are necessary to fully answer the questions raised by the phase II trials.In order to progress the field, the European Society of Cardiology has recently established a Working Group on Cardiovascular Regenerative and Reparative Medicine—the aim of which is to develop the field beyond the current hiatus that now exists. We eagerly await the guidance from this group and the release of definitive results that will help decide which areas of regenerative medicine should be pursued and importantly what should be dropped.


Magnetic reconnections play essential roles in space, astrophysical, and laboratory plasmas, where the anti-parallel magnetic field components re-connect and the magnetic energy is converted to the plasma energy as Alfvénic out flows. Although the electron dynamics is considered to be essential, it is highly challenging to observe electron scale reconnections. Here we show the experimental results on an electron scale reconnection driven by the electron dynamics in laser-produced plasmas. We apply a weak-external magnetic field in the direction perpendicular to the plasma propagation, where the magnetic field is directly coupled with only the electrons but not for the ions. Since the kinetic pressure of plasma is much larger than the magnetic pressure, the magnetic field is distorted and locally anti-parallel. We observe plasma collimations, cusp and plasmoid like features with optical diagnostics. The plasmoid propagates at the electron Alfvén velocity, indicating a reconnection driven by the electron dynamics. Magnetic reconnection is the process of releasing energy by magnetized and space plasma. Here the authors report experimental observation of magnetic reconnection in laser-produced plasma and the role of electron scaling on reconnection. It governs various phenomena such as magnetospheric substorms, stellar and solar flares, and their winds and coronal heatings. The magnetic reconnection can also play essential role in particle acceleration in the presence of collisionless shocks5. It has been widely believed that the electron dynamics is essential in the triggering processes of the magnetic reconnections8, however, it is highly challenging to observe the electron features due to their small spatial and temporal scales both in space and laboratory plasmas10. The first electron scale measurements of magnetic reconnection in space plasma were reported very recently10. However, as the space observations are provided with a (few) spacecrafts in situ, there is no global observation or imaging of magnetic reconnections. With the in situ observations the structure of the X-line and jets are provided with numerical simulations or schematic figures. On the other hand, imaging of solar flares provide us global structures of magnetic reconnections such as cusp and plasmoid11, although it is impossible to resolve the electron scale dynamics. Even though it is difficult to simultaneously observe electron and ion scale phenomena due to the large scale difference between these two species, we can properly model some aspects of the physical processes, where the electron kinetics governs the macroscopic structures in laboratory.Magnetic reconnection is a fundamental factor in space and astrophysical plasmas, where anti-parallel magnetic field components reconnect and release the magnetic energy as the plasma kinetic energy1. While in space plasmas a single or a few observation points provide the magnetic field data, the magnetic reconnection experiments in the laboratory provide multiple possible observations, which allow the imaging of the reconnection regions. Recently, fast reconnections have been observed in laser-produced plasmas18. In these experiments, multiple beams are focused on a solid target with small separations, and then the baroclinic magnetic fields are generated surrounding the laser-produced plasmas, resulting in magnetic reconnection with the anti-parallel field geometry. These reconnections are strongly driven by the expanding plasmas that collide each other19. Our experimental approach is completely different from the previous studies with high-power lasers, where the laser–matter interactions and the self-generated magnetic fields play an essential role. We focus on electron dynamics by using a weak external field produced by a permanent magnet. Under the influence of this field, that is perpendicular to the plasma flow propagation axis, it can be collimated due to the distortion of the magnetic field20. We adjust the field strength so that the electrons are magnetized but not the ions, while we keep the system size much larger than the ion inertial length, c is the speed of light and ωpi is the ion plasma frequency. This system is directly applicable to the magnetic reconnection driven by the electron dynamics.The magnetic reconnections have also been investigated with magnetic confinement deviceHere we report the experimental results on an electron scale reconnection governed by the electron dynamics in laser-produced plasmas. We separate the electron scale from the ion scale by a weak external magnetic field. The magnetic field is strong enough to magnetize the electrons but not the ions; the magnetic field is not directly coupled with ions. We have observed thin plasma structures and plasmoid like features with optical diagnostics, indicating a reconnection at microscopic scale driven by the electron dynamics. The plasmoid is accelerated due to the reconnection up to the electron Alfvén velocity, indicating efficient acceleration of electrons.Figure −1. This is consistent with the SOP result (not shown). Using this as the ion bulk velocity, the ratio between the kinetic pressure to the magnetic pressure is estimated as ni is the ion density, mi is the ion mass, vi is the ion velocity, μ0 is the magnetic permeability in vacuum, and we assume average mass and charge of protons and fully ionized carbon ions. Even though the kinetic energy is much larger than the magnetic energy, such weak magnetic field affects the plasma propagation. With vi = 500 km s−1 and B = 0.3 T the proton gyroradius is e is the element charge and mp is the proton mass, and that of the carbon ion with its charge of Z = 6 and mass of mc = 12mp is simply twice of the proton’s. Besides, the electron gyroradius with the same velocity is From the snapshot of the electron density map we estimate the plasma velocity; the fringe shifts are recognized at 8 mm from the target in 15 ns in Fig. B) in vacuum a plasma propagates in the direction perpendicular to the magnetic field. When the kinetic pressure is much larger than the magnetic pressure, the magnetic field will be stretched by the plasma. Stretching the field induces a new magnetic field as in Fig. E) is excited across the distorted magnetic field . In the latter case, it is not necessary to assume that the plasma is actually faster in the presence of the external magnetic field. This can be confirmed with our simulations in Supplementary Figures In Fig. 24. If this plasmoid propagates at Alfvén velocity, one can conclude that the plasmoid results from the reconnection. In our system only electrons are directly coupled with the magnetic field, and thus, the outflow velocity is relevant to the electron dynamics. The electron Alfvén speed is defined with the electron mass as B = 0.3 T and the electron density from Fig. 19 cm−3 but the collimated electron density is about 2–5 × 1019 cm−3. We cannot obtain the density from the interferogram of the same shot as Fig. ne = 2–5 × 1019 cm−3 at the plasma propagation axis in Fig. ceA = 40–63 km s−1. This is very close the outflow velocity in Fig. Cusps and plasmoids are key features of the reconnection. Plasmamoids play a fundametal role in the fast reconnections27, micro magnetospheres31, plasma jets34, and the reconnections in electron scales8. For instance, lunar surface magnetic fields have typically smaller size than ion gyroradius of the solar wind; it is considered that the electron dynamics plays essential roles on their interactions with the solar wind31.In this paper we have discussed a magnetic reconnection driven by electron dynamics in a laser-produced plasma. In the presence of a weak-perpendicular magnetic field, where only electrons are magnetized, plasma collimation is observed. Since the ions in our system are not magnetized, the structure formation solely observed in the presence of the field is an evidence that the electrons dynamics controlling the macroscopic structure. Our experimental results with the ambient plasma show the essential aspects of reconnections, i.e., the cusp and the Alfvénic outflows. These results bring tremendous benefit to various fields of science and engineering, such as magnetic sailsB ~ 0.7 T at the surface) was located ~5 mm below the target center, giving a magnetic field B ~ 0.3 T perpendicular to the target normal. Since the diameter of the magnet was 30 mm, the field where the plasma propagates was effectively uniform. The laser beams were separated by 100–200 μm in order to make the plasma directional21. The spatial and temporal evolutions of the rear-side plasmas were observed by transverse optical diagnostics with 2D time resolved detectors (self-emission and interferometry) and streaked optical pyrometer (SOP). The interferometer was a modified Nomarski type35, and the self-emission was taken at the wavelength of 450 nm.The experiment was performed with Gekko XII HIPER laser system at the Institute of Laser Engineering, Osaka university. The main laser beams  were used to irradiate a plastic plannar  to produce a fast plasma in the rear side of the target. Plasma is also created on the side of laser irradiation, we mainly focus on the rear-side plasmas. Figures The custom particle-in-cell code used to generate the simulation results in the current study is available from the corresponding author on reasonable request.Supplementary InformationPeer Review File


RQH (Red Queen hypothesis), which argues that hosts need to be continuously finding new ways to avoid parasites that are able to infect common host genotypes, has been at the center of discussions on the maintenance of sex. This is because diversity is favored under the host–parasite coevolution based on negative frequency‐dependent selection, and sexual reproduction is a mechanism that generates genetic diversity in the host population. Together with parasite infections, sexual organisms are usually under sexual selection, which leads to mating skew or mating success biased toward males with a particular phenotype. Thus, strong mating skew would affect genetic variance in a population and should affect the benefit of the RQH. However, most models have investigated the RQH under a random mating system and not under mating skew. In this study, I show that sexual selection and the resultant mating skew may increase parasite load in the hosts. An IBM , which included host–parasite interactions and sexual selection among hosts, demonstrates that mating skew influenced parasite infection in the hosts under various conditions. Moreover, the IBM showed that the mating skew evolves easily in cases of male–male competition and female mate choice, even though it imposes an increased risk of parasite infection on the hosts. These findings indicated that whether the RQH favored sexual reproduction depended on the condition of mating skew. That is, consideration of the host mating system would provide further understanding of conditions in which the RQH favors sexual reproduction in real organisms.The  Infectious disease and parasite load are pervasive in nature and impose a heavy cost on host species Poulin . Given tIn general, the maintenance of sex becomes problematic under the assumption that paternal investment in the offspring is minimal Kawatsu ,b, as prRecently, theoretical studies have shown that the RQH may promote the evolution of female mate choice for male disease resistance  was developed, which included host–parasite interactions and sexual selection in the host population, and the RQH was examined under different degrees of mating skew and genetic correlations between the health of the males and the male trait that was under sexual selection. Based on the results, the possibility of the evolution of mating skew with varying genetic correlations between the male traits and health was examined. In a second analysis, to investigate whether the evolution of mating skew in the host species differed between types of sexual selection; that is, male–male competition for mates and female mate choice, the IBM was extended to describe both a case in which mating bias was associated only with male–male competition and a case in which female preference for male traits also affected the evolution of mating bias. Discussion of these analyses should shed light on the demographic effects and evolutionary outcomes of mating skew in host organisms coevolving with parasites.NH* and NP*, respectively. Hosts were assumed to be obligatory sexual and anisogamous species , whereas parasites reproduced asexually. The model consisted of a two‐step selection phase: a host–parasite interaction and a mating interaction in the hosts. The host–parasite interaction was mediated by a haplotype of host immunity and parasite infectivity. Following the interspecific interaction, host mating proceeded; each host female was modeled to mate with one male depending on his genetic quality.An IBM that tracked the coevolutionary dynamics between hosts and parasites under sexual selection for host males was constructed. In the model, it was assumed that selection acted on haploid organisms, and the host and parasite population consisted of a constant number of individuals, The model assumed that outcomes of the interspecific interaction between a host and a parasite  were mediated by a mechanism of self‐ versus non‐self‐recognition that was controlled by a haplotype of host immunity and parasite infectivity. Both haplotypes were simply determined by two loci with two alleles, and each allele was labeled either 0 or 1 . For the recognition mechanism, host immunity could recognize parasites with surface molecules different from those of the host cell Frank  and effeGH,i was randomly exposed to parasites with the infectivity haplotypes GP,j depending on their frequency and that interactions resulting in infection reduced host fitness  and max, respectively.After interactions between the two species, each host and parasite was randomly selected to form a reproductive population according to their survival rates. In addition, to maintain the size of the reproductive population of the host and parasite below Y. An expression of Y was associated with a continuous value of an allele of the male y trait and his health or state of infection to some degree; that is, the male phenotype Y could be referred to as a condition‐dependent sexually selected trait . In cases of male–male competition, a host male randomly attempted to mate with a certain number of females (the number was denoted by M), and for each female, the male with the highest Y was the successful mate. In this simulation, the value of mating trait m was modeled to a range from 0.0 to 1.0 and determined the number of mating attempts as M = mNH. The higher the value of m in the population, the less likely that poor‐quality males would find a mate. For the female mate choice, a host female randomly screened M males by the male Y phenotype value and mated with the male with the highest Y value. The number of males screened was determined by the value of her mating trait, m, in the same way as for the male–male competition. Therefore, for both cases of sexual selection, the mean value of the host mating trait strongly associated with the degree of mating skew in the host population: Mating success should be more biased toward the males with the higher male phenotype value, as the mean value of mating trait increases in the population.Next, the degree of mating skew that could evolve under the different correlation y trait were added by mutation displacement based on a normal distribution with a mean of 0.0 and standard deviation of 0.01. Mutations between alleles 0 and 1 at immunity and infectivity loci occurred mutually at a rate of 1.0 × 10−5. In the second simulation, alleles of the mating trait m were also added by mutational displacement in the same way as the mutation of the male trait y.After the mating interaction, each host female produced 20 offspring . Host offspring inherited relevant alleles from both parents with equal probability and free recombination due to sexual reproduction, and offspring sex was determined randomly. For the parasite reproduction, each parasite female also produced 20 offspring. However, because of asexual reproduction, the offspring were all female and clonally inherited the alleles from their mother, except for mutations. Mutations occurred at the time of offspring production. Alleles of the male continuous μ varied from 0.0 to 1.0, and the value of the correlation ρ varied from 0.0 to 1.0. In the second simulation, the mean value of the mating trait m in the host population, and the correlation ρ varied from 0.0 to 1.0, and this was recorded to examine the effect of the correlation on the evolution of the mating trait. If not otherwise specified, all other conditions were as follows: host and parasite population sizes were N̂H = N̂P = 500; the scale of selection by parasite infection was θH = 0.25; the scale of selection by host resistance θP = 0.75; the value of male trait at the initial condition was 0.0; the value of mating trait at the initial condition was m = 0.01.Each simulation ran for 2000 generations and iterated 50 times for each parameter set. Two and eight parasite generations per single host generation were used in all simulation runs . The mean rate of infection in the host population and the frequency of recognition loci (host immunity and parasite infectivity) were recorded. In the first simulation, to compare the effects of mating skew and the correlation between male phenotype and state of infection, the value of the degree of mating skew μ = ρ = 0.0; Fig. Figure μ ≥ 0.8) for both parasite generation times  in longer parasite generation times , the infection rate decreased as the genetic correlation between the male trait and male condition strengthened , regardless of the value of correlation. On the other hand, in the case of female mate choice, an increase in the correlation decreased the value of the mating trait under both parasite generation timescales. However, the mating trait evolved to be higher than its initial value except in the case of the highest value of the correlation . Additionally, a higher mating trait was more likely to evolve in cases of male–male competition than in cases of female mate choice, but the difference in parasite generation timescales had little effect on the evolution of the mating trait.The results of first simulation suggest that mating skew could worsen infections in the host population because it changed the coevolutionary relationship between hosts and parasites. The second simulation was carried out to investigate how strong mating skews were able to evolve, even with the cost of intensified parasite infection. Figure ρ = 0.0 compared to the other results for both parasite generation timescales. Moreover, the host population in the male–male competition system suffered more serious infections compared to the random mating system (represented by the dotted lines) for all the correlations in the long‐ and short‐term parasite generations. On the other hand, in the case of female mate choice, the mean infection rate was highest when ρ = 0.0 and lowest when ρ = 1.0 compared the results of the others for both timescales of parasite generations. The host population of female mate choice also suffered from more infections than those from the random mating system for all the correlations, other than ρ = 1.0 in the long‐ and short‐term generations. The mean infection rate of the host population was also higher in cases of male–male competition than in female mate choice, and it differed among the parasite generations times; the differences in the results of sexual selection and the random mating system were smaller for long parasite generation times , no mating skews evolved in the case of female mate choice (Fig. The results imply that an increase in mating skew may impose a cost of increased infection on the host population. Nevertheless, analysis of the second simulation demonstrated that when the sexually selected phenotype conveyed some information of male immunity, mating skew evolved in cases of male–male competition and female mate choice Fig. . As a reice Fig. . This ocice Fig. . Thus, tThe analyses of the IBMs also provided a new understanding of the relationship between the RQH and sexual selection. The results from the second model demonstrated that mating skew evolved more easily in male–male competition than in female mate choice Fig. . This coThe evidence based on the simulation analyses revealed that when considering sexual selection and the resultant evolution of mating skew, the effects of the RQH on hosts should depend on its mating system. This perspective will aid our understanding of conditions in which the RQH favors sexual reproduction in real organisms. Many empirical studies have confirmed the RQH and benefits of sexual reproduction of hosts under host–parasite coevolution. These studies involved diverse host–parasite systems, including a freshwater snail and a parasitic trematode Lively , psychidNone declared.