The present disclosure relates to an antibody production assisting method and an antibody production assisting program.
In recent years, studies in research on antibodies produced by culturing cells have been advanced. The specification of U.S. Pat. No. 8,911,964 (PTL 1) discloses a technique related to production of antibodies by using culture of Chinese hamster ovary (CHO) cells. PTL 1 discloses that manufacturers of antibodies monitor glucose concentrations and feedback the monitored results.
The manufacturers of the antibodies preferably set appropriate culture conditions in the production of the antibodies. However, it is necessary for the manufacturers to set culture conditions on the basis of the limited monitored results. It has been a practice for the manufacturers to set the culture conditions on the basis of experience of the manufacturers themselves. Therefore, it may be difficult for some manufactures to set appropriate culture conditions, and in such a case, a problem may occur in that it is difficult to produce the antibodies.
An object of the present disclosure, which has been made to solve such a problem, is to assist production of antibodies.
An antibody production assisting method according to an aspect of the present disclosure is a method for assisting production of an antibody. The antibody production assisting method includes: acquiring time-series data that indicates, in in chronological order, a plurality of metabolite data and a culture parameter, the plurality of metabolite data each corresponding to a respective amount of a plurality of metabolites generated by culturing a cell line for producing the antibody, the culture parameter being detected from the cell line in culture. Also, the antibody production assisting method includes acquiring a degree of relevance between the culture parameter and each of the plurality of metabolites on the basis of the time-series data. Furthermore, the antibody production assisting method includes generating display data based on the degree of relevance.
Additionally, an antibody production assisting program according to an aspect of the present disclosure is a program for assisting production of an antibody. The antibody production assisting program causes a computer to execute acquiring of time-series data that indicates, in in chronological order, a plurality of metabolite data and a culture parameter, the plurality of metabolite data each corresponding to a respective amount of a plurality of metabolites generated by culturing a cell line for producing the antibody, the culture parameter being detected from the cell line in culture. Also, the antibody production assisting program causes the computer to execute acquiring of a degree of relevance between the culture parameter and each of the plurality of metabolites on the basis of the time-series data. Furthermore, the antibody production assisting program causes the computer to execute generating of display data based on the degree of relevance.
In the present disclosure, the display data based on the degree of relevance between the culture parameter and each of the plurality of metabolites is generated. Therefore, a manufacturer can presume a culture condition to be adjusted by viewing an image based on the display data. According to the present disclosure, it is thus possible to assist production of the antibody.
Hereinafter, an embodiment of the present disclosure will be described in detail with reference to the drawings. Note that the same reference signs will be applied to the same or corresponding parts in the drawings and description thereof will not be repeated.
In the present embodiment, a manufacturer of an antibody (hereinafter, simply referred to as a “manufacturer” or a “user”) sets an appropriate culture condition, a cultivation device cultures a cell line under the culture condition and extracts an antibody from the cultured cell line. In such a method for producing an antibody, it is preferable that an appropriate culture condition be set. The setting of the culture condition depends on a level of experience of the manufacturer himself/herself in many cases, and it may be difficult for a less experienced manufacturer to set an appropriate culture condition. Thus, an antibody production assisting method according to the present embodiment assists production of an antibody to be used in an antibody drug. More specifically, the antibody production assisting method allows the manufacturer to predict a culture condition to be set and a value of the culture condition.
Culture device 2 cultures a cell line and extracts an antibody from the cultured cell line. The cell line is, for example, a CHO cell. Examples of a culturing method include alternating tangential flow (ATF) culture as a kind of perfusion culturing method, fed-batch culture as a kind of feeding culturing method, and the like. Particularly, since a perfusion system is employed in the ATF culture, it is possible for a manufacturer to achieve continuous culture, that is, to culture a cell line in a long-term culture period. In the present embodiment, culture device 2 employs the ATF culturing method. It is possible to achieve long-term cell culture by the ATF culturing method being employed. In the present embodiment, it is assumed that the cell line is cultured for a 30-day culture period.
Also, a culture condition 3 that the manufacturer can set is, for example, at least one of an amount of basal medium, a composition of a basal medium, a flow rate of breeding, an amount of feed medium, a composition of a feed medium, a perfusion rate, a stirring speed, an amount of air blowing, an amount of carbon dioxide blowing, an amount of alkali addition, an amount of defoaming agent addition, and the like. The manufacturer sets at least one of these culture conditions as a culture condition through an operation or the like of a device corresponding to the culture condition. For the amount of carbon dioxide blowing, for example, the manufacturer sets the amount of carbon dioxide blowing by operating a carbon dioxide blowing device.
Sensor group 4 is composed of one or more sensors. Each of the one or more sensors detects a culture parameter corresponding to the sensor. The culture parameter includes a cell density, a cell viability, a cell diameter, a specific growth speed, an antibody production speed, pH, a temperature, dissolved oxygen (DO), an oxygen partial pressure, a carbon dioxide partial pressure, or the like. The specific growth speed is a proportion of an amount of increase in cells per unit time calculated from a difference from a previous (one day before, for example) cell density, or the like.
The manufacturer extracts a part of culture solution for the cell line cultured in culture device 2. Then, the manufacturer causes analysis device 6 to analyze the extracted part of cell culture solution as a sample. At that time, analysis device 6 performs an operation for separating a culture solution supernatant and cells, a pre-analysis treatment is performed on each of them, and analysis device 6 is then caused to perform analysis. Analysis device 6 is, for example, a liquid chromatograph-mass spectrometry/mass spectrometry (LC-MS/MS). Also, the manufacturer also inputs the date and the time of the analysis to analysis device 6.
Analysis device 6 can measure the amount of each of metabolites (171 metabolites, for example) generated by culturing a cell line. The manufacturer can select the number of metabolites to be measured and the types of metabolites. Then, analysis device 6 derives an analysis result (the amount of each of the plurality of metabolites) in an associated manner with the input date and time. The analysis result includes a plurality of (171, for example) metabolite data that indicate, in in chronological order, the amount of each of the plurality of metabolites generated by culturing the cell line. The metabolite data may be data that directly indicates the amount of each of the metabolites, or may be data that indirectly indicates it. In other words, the plurality of metabolite data are data corresponding to the amount of each of the plurality of metabolites. In the present embodiment, the manufacturer causes analysis device 6 to analyze the sample once a day and derive an analysis result. Also, the manufacturer may cause a display device (not illustrated) of analysis device 6 to display the analysis result or may not cause the display device to display it every time the analysis result is derived. In this manner, the manufacturer causes analysis device 6 to derive the analysis results for the culture period (that is, for 30 days).
Also, the manufacturer acquires a culture parameter in the culture period on the basis of a detection result of sensor group 4. For example, the manufacturer acquires the culture parameter when the cells cultured by culture device 2 are collected.
Input device 40 is a device such as a keyboard or a mouse, for example, and receives a command from the manufacturer. Display device 30 is composed of a liquid crystal display (LCD) panel, for example, and displays information for the manufacturer. In a case where a touch panel is used as a user interface, input device 40 and display device 30 are integrally formed.
Information processing device 100 generates display data by executing predetermined processing on data transmitted from input device 40. Information processing device 100 may be implemented by a general-purpose computer or may be implemented by a computer dedicated for information processing device 100, for example. The general-purpose computer may be a personal computer (PC) or may be a tablet, for example. Note that at least a part of computing for generating the display data may be implemented as software by a central processing unit (CPU) of information processing device 100 or may be implemented as hardware that performs processing independently from the CPU.
The manufacturer inputs the analysis results in the culture period and the culture parameters to input device 40. In the present embodiment, the manufacturer inputs the analysis results for 30 days and the culture parameters for 30 days corresponding to the analysis results to input device 40. Note that not all the analysis results for 30 days are necessarily be input, and analysis results for predetermined days out of the 30 days (analysis results for 15 days, for example), for example, may be input. Information processing device 100 acquires the data input from input device 40 as time-series data for 30 days. In the present embodiment, the time-series data refers to the analysis results for 30 days and each culture parameter for the 30 days.
Information processing device 100 and computing device 200 are configured to be able to communicate via a network 50. Once the time-series data is acquired from input device 40, then information processing device 100 outputs it to computing device 200. Computing device 200 executes predetermined computing, which will be described later, and outputs the computing result to information processing device 100. Information processing device 100 generates display data based on the computing result.
Communication I/F 168 is an interface for communicating with computing device 200. Display I/F 170 is an interface for communicating with display device 30. Input I/F 172 is an interface for communicating with input device 40.
ROM 162 stores a program to be executed by CPU 160. RAM 164 can temporarily store data generated by CPU 160 executing the program and data input via communication I/F 168. RAM 164 can function as a transitory data memory used as a work area. HDD 166 is a non-volatile storage device. A semiconductor storage device such as a flash memory may be employed instead of HDD 166.
The program stored in ROM 162 may be stored in a non-transitory recording medium and may be distributed as a program product. Alternatively, the program may be provided by an information provider as a product program that can be downloaded through what is called the Internet or the like. Information processing device 100 reads the program provided by the recording medium, the Internet, or the like. Information processing device 100 stores the read program in a predetermined storage region (in ROM 162, for example). CPU 160 can execute various kinds of processing by executing the program.
Next, culture parameters and the like will be described.
In
In the examples in
Under this presumption, it is assumed that the manufacturer has also checked an oxygen partial pressure as a culture parameter.
In such a process of manufacturing the antibody, the cultured cell line is likely to be affected by a change in environment inside a culture tank of a first culture device 10 and the like, and variations in metabolites frequently occur. Thus, it is preferable for the manufacturer to set (adjust) the aforementioned culture conditions such that the variations in the culture parameters illustrated in
Incidentally, metabolites (glucose, a lactic acid, and the like in
Computing device 200 receives the request signal and the time-series data. Computing device 200 executes correlation analysis on the time-series data. Although a method using a Pearson product-moment correlation coefficient or a Spearman's or Kendall's rank correlation coefficient is used as a method for the correlation analysis in accordance with properties of analysis data, a method other than these may also be used as a method for analyzing a correlation between two different values. Computing device 200 generates data of degrees of relevance through the correlation analysis. The data of degrees of relevance is data indicating degrees of relevance between the culture parameters and each of the plurality of metabolites. Computing device 200 transmits the data of degrees of relevance to information processing device 100.
Request unit 104 of information processing device 100 acquires the data of degrees of relevance. Request unit 104 transmits the data of degrees of relevance to display control unit 106. Display control unit 106 generates display data based on the data of degrees of relevance. Display control unit 106 causes display device 30 to display an image based on the display data. Note that information processing device 100 rather than computing device 200 may execute the correlation analysis.
Also, identification information A to E for the metabolic pathway of the metabolite corresponding to the section for the metabolic pathway is shown in the section for the metabolic pathway. Additionally, a degree of relevance between the metabolite and the culture parameter (oxygen partial pressure) corresponding to the section for the degree of relevance is shown in the section for the degree of relevance. In addition, a p value for the degree of relevance corresponding to the section for the p value is shown in the section for the “p value”.
In the right table in
Additionally, the left table in
Also, analysis device 6 measures the amount of each of the 171 kinds of metabolites as described above. Thus, display device 30 may display a degree of relevance and the like of each of the 171 kinds of metabolites. However, display of metabolites with low degrees of relevance with the culture parameters are not very useful for the manufacturer. Also, it becomes difficult for the manufacturer to see the correspondence image if degrees of relevance are displayed for a large number of metabolites.
Thus, information processing device 100 extracts degrees of relevance that satisfy a condition for a degree of relevance indicating that a degree of relevance with a culture parameter is high in the present embodiment. Here, the condition for a degree of relevance in the present embodiment is a condition that the p value is less than 0.05 and an absolute value of the degree of relevance is more than 0.7.
In this manner, the correspondence image in
Incidentally, the manufacturer can cause information processing device 100 to create a metabolic map. The metabolic map is a map that shows metabolites, metabolic pathways of the metabolites, and the like. Also, an application for assisting creation of the metabolic map has been downloaded on information processing device 100, and the manufacturer creates the metabolic map by using the application for assisting creation.
Also, glucose and a lactic acid are shown as metabolites, and names of other metabolites are omitted in the example in
Also, the manufacturer can estimate a culture condition to be adjusted by viewing the correspondence image in
Next, information processing device 100 generates display data on the basis of the data of degrees of relevance in Step S6. Then, information processing device 100 displays a correspondence image based on the display data on display device 30 in Step S8.
Next, other display images of the correspondence image displayed by display device 30 will be described. For example, an image (first image) of only a metabolic map in the surrounding of a metabolite may be displayed while metabolic map at the other location may not be displayed once the manufacturer designates a block of a name of the metabolite from among names of the plurality of metabolites displayed on the correspondence image in
Also, information processing device 100 may display the metabolic map displayed in a case where designation is made from among the plurality of metabolites as an image (second image) in a different manner from the metabolic map at the other location.
Also, information processing device 100 may display a third image including a name of a metabolic pathway of the designated metabolite.
Also, information processing device 100 may display a fourth image such that the designated metabolite is identifiable in the metabolic map.
Also, the case where there are multiple metabolites (thirteen in the example in
Next, time-series data of multiple attributes will be described. Among cells with complicated gene sequences, such as a CHO cell line that has acquired an indefinite proliferative potential, some created cells may not have intended gene sequences. Therefore, significant differences may occur in culture results even if a plurality of cell lines are cultured under mutually the same culture conditions. Hereinafter, two cell lines will be referred to as a cell line A and a cell line B. In the antibody production assisting method according to the present embodiment, the manufacturer is allowed to presume a culture condition to be adjusted in culture device 2 such that an antibody produced from cell line A and an antibody produced from cell line B are appropriately produced. In the present embodiment, the plurality of first metabolite data that indicate, in chronological order, each of amounts of a plurality of metabolites generated by culturing cell line A and the plurality of second metabolite data that indicate, in chronological order, each of amounts of a plurality of metabolites generated by culturing cell line B are used. Then, information processing device 100 specifies a target metabolite caused by a difference between the first metabolite data and the second metabolite data and displays an image based on the target metabolite.
In
In the example in
In the process of manufacturing the antibody, cell line A and cell line B to be cultured are likely to be affected by a change in environment inside the culture tank of culture device 2 and the like, and variations in metabolites frequently occur. Thus, it is preferable that the manufacturer set (adjust) the culture condition in culture device 2 such that cell line A and cell line B have equivalent trends of variations in amounts of metabolites. However, it is necessary for the manufacturer to set the culture condition in culture device 2 on the basis of the limited monitored results (the monitored results in
Incidentally, the metabolites (metabolite b1, metabolite b5, and the like in
In this embodiment, the aforementioned first metabolite data and second metabolite data are input to input unit 102 illustrated in
Computing device 200 receives the request signal, the first metabolite data, and the second metabolite data. Computing device 200 executes principal component analysis on the first metabolite data and the second metabolite data. Computing device 200 generates focused metabolite data through the principal component analysis. The focused metabolite data is data indicating a target metabolite or the like that is attributable to a difference between the first metabolite data and the second metabolite data. Computing device 200 transmits the focused metabolite data to information processing device 100.
Request unit 104 of information processing device 100 acquires the focused metabolite data. Request unit 104 transmit the focused metabolite data to display control unit 106. Display control unit 106 generates display data based on the focused metabolite data. Display control unit 106 causes display device 30 to display an image based on the display data.
As described in
In the example in
In the example in
Also, plots of cell line A are distributed in a positive region of the second principal component axis. Additionally, plots of cell line B are distributed in a negative region of the second principal component axis. Therefore, the second principal component axis is an axis that can explain the culture parameter (or the culture condition).
In the example in
In the example in
It is only necessary for the manufacture to view the names of the metabolites inside frame XA3 in
Also, the manufacturer can estimate the culture condition to be adjusted in culture device 2 by viewing the fifth image in
Next, other display images that display device 30 displays will be described. For example, once the manufacturer designates a block of a name of a metabolite from among names of metabolites b1 to b12 (including target metabolite b7) displayed in the fifth image in
Next, other display images of images to be displayed by display device 30 will be described. For example, the configuration in which the image of only the metabolic map around target metabolite b7 that has been designated in the fifth image in
However, information processing device 100 may display the metabolic map displayed in a case where designation has been made from among the plurality of metabolites as an image (seventh image) in a different manner from the metabolic map at the other location.
Also, information processing device 100 may display an eighth image (see
Also, information processing device 100 may display the eighth image such that the designated metabolite is identifiable in the metabolic map.
Also, the case where there are multiple (twelve in the example in
Also, the configuration in which the cell line with the first attribute is cell line A and the cell line with the second attribute is cell line B has been described in this embodiment. However, the cell line with the first attribute and the cell line with the second attribute may be other fine part lines. For example, the cell line with the first attribute may be a cell line cultured under a first culture condition, and the cell line with the second attribute may be a cell line cultured under a second culture condition (which is a culture condition that is different from the first culture condition). With such a configuration, the manufacturer can presume which of the first culture condition and the second culture condition is an appropriate culture condition or the like from a displayed specific cell line. Also, the number of attributes may be three or more.
(1) In the aforementioned embodiment, the configuration in which information processing device 100 generates the display data and causes display device 30 to display the image based on the display data has been described. However, a configuration in which information processing device 100 does not cause display device 30 to display the image may be employed. In a case of such a configuration, the manufacturer causes a recording medium that can record information thereon to be connected to information processing device 100, for example. Then, information processing device 100 causes the recording medium to store the display data. The manufacturer may connect the recording medium storing the display data thereon to a different display device and cause the different display device to display the image based on the display data. Even with such a configuration, effects that are similar to those of the aforementioned embodiment are achieved.
(2) In the aforementioned embodiment, the configuration in which analysis device 6 and information processing device 100 are separate devices has been described. However, analysis device 6 may execute at least a part of processing executed by information processing device 100. For example, analysis device 6 may display the image that display device 30 is caused to display as described above.
(3) In the aforementioned embodiment, the example in which single information processing device 100 executes all the processes has been described. However, one or multiple processes may be executed by another information processing device. The plurality of information processing device may be disposed at remote locations from each other. For example, a certain computer may execute the acquisition of the degrees of relevance, and another computer disposed at a remote location may execute the generation of the display data. A plurality of other computers may be present and perform generation of mutually different display data.
(4) In the aforementioned embodiment, the example in which the metabolite data obtained from the plurality of cell lines are compared and multivariable analysis (principal component analysis) is used to determine the target metabolite has been described. However, correlation analysis may be performed on time-series metabolite data obtained from a single cell line to determine a necessary time range, multivariable analysis may be performed on metabolite data in the time range, and a relationship between the culture parameter and the metabolite data may thus be obtained.
Those skilled in the art will understand that the aforementioned plurality of illustrative embodiments are specific examples of the following aspects.
An antibody production assisting method according to an aspect is an antibody production assisting method for assisting production of an antibody, the method including: acquiring time-series data that indicates, in in chronological order, a plurality of metabolite data and a culture parameter, the plurality of metabolite data each corresponding to a respective amount of a plurality of metabolites generated by culturing a cell line for producing the antibody, the culture parameter being detected from the cell line in culture; acquiring a degree of relevance between the culture parameter and each of the plurality of metabolites on the basis of the time-series data; and generating display data based on the degree of relevance.
With such a configuration, the display data based on the degree of relevance is generated. Therefore, the manufacturer can presume a culture condition to be adjusted by viewing an image based on the display data, and as a result, it is possible to assist production of the antibody.
The antibody production assisting method described in the first clause further includes: causing a display device to display an image based on the display data.
With such a configuration, an image related to the display data based on the degree of relevance is displayed. Therefore, the manufacturer can presume a culture condition to be adjusted by viewing the image.
In the antibody production assisting method described in the second clause, the acquiring of the time-series data includes acquiring a plurality of first metabolite data and a plurality of second metabolite data, each of the plurality of first metabolite data corresponding to a respective amount of a plurality of metabolites generated by culturing a cell line with a first attribute, each of the plurality of second metabolite data corresponding to a respective amount of a plurality of metabolites generated by culturing a cell line with a second attribute, the antibody production assisting method further includes: specifying a difference between the first metabolite data and the second metabolite data; and specifying a target metabolite caused by the difference, and the causing of the display device to display includes displaying an image based on the target metabolite.
With such a configuration, the manufacturer can recognize the target metabolite that is caused by the difference between the first metabolite data and the second metabolite data.
In the antibody production assisting method described in the second clause or the third clause, the causing of the display device to display includes displaying, for the culture parameter, a correspondence image in which each of names of the plurality of metabolites is associated with a degree of relevance between the culture parameter and each of the plurality of metabolites.
With such a configuration, the manufacturer can presume a culture condition to be adjusted by viewing the correspondence image.
In the antibody production assisting method described in the fourth clause, the antibody production assisting method further includes: extracting a degree of relevance that satisfies a condition for a degree of relevance indicating that a degree of relevance with the culture parameter is high from among all calculated degrees of relevance, and the correspondence image is an image in which the degree of relevance that satisfies the condition for a degree of relevance is associated with a name of a metabolite associated with the degree of relevance.
With such a configuration, the metabolite with a high degree of relevance with the culture parameter is displayed, and the manufacturer can thus presume a culture condition to be adjusted on the basis of the metabolite.
In the antibody production assisting method described in the fifth clause, the causing of the display device to display includes causing the display device to display the correspondence image in a different manner for each metabolic pathway of the metabolite for the metabolite corresponding to the degree of relevance that satisfies the condition for a degree of relevance.
With such a configuration, the metabolite with a high degree of relevance with the culture parameter is displayed, and the manufacturer can thus presume a culture condition to be adjusted on the basis of the metabolite.
In the antibody production assisting method described in the fifth clause or the sixth clause, the causing of the display device to display includes displaying a metabolic map around the metabolite corresponding to the degree of relevance that satisfies the condition for a degree of relevance and a metabolic map at another location in different manners from each other.
With such a configuration, the manufacturer can recognize the metabolic map around the metabolite with a high degree of relevance with the culture parameter. Therefore, the manufacturer can more clearly presume a culture condition to be adjusted on the basis of the metabolic map.
In the antibody production assisting method described in the fifth clause or the sixth clause, the causing of the display device to display includes displaying a metabolic map around the metabolite corresponding to the degree of relevance that satisfies the condition for a degree of relevance and not displaying a metabolic map at another location.
With such a configuration, the manufacturer can recognize the metabolic map around the metabolite with a high degree of relevance with the culture parameter. Therefore, the manufacturer can more clearly presume a culture condition to be adjusted on the basis of the metabolic map.
In the antibody production assisting method described in any one of the fifth clause to the eighth clause, the causing of the display device to display includes displaying a name of a metabolic pathway of the metabolite corresponding to the degree of relevance that satisfies the condition for a degree of relevance.
With such a configuration, the manufacturer can recognize the metabolic pathway of the metabolite with a high degree of relevance with the culture parameter. Therefore, the manufacturer can more clearly presume a culture condition to be adjusted on the basis of the metabolic pathway.
In the antibody production assisting method described in any one of the fourth clause to the ninth clause, the causing of the display device to display includes displaying the metabolite corresponding to the degree of relevance that satisfies the condition for a degree of relevance in an identifiable manner in a metabolic map.
With such a configuration, the manufacturer can recognize the metabolite with a high degree of relevance with the culture parameter. Therefore, the manufacturer can more clearly presume a culture condition to be adjusted on the basis of the metabolite.
An antibody production assisting program according to an aspect is a program for assisting production of an antibody, the program causing a computer to execute: acquiring of time-series data that indicates, in in chronological order, a plurality of metabolite data and a culture parameter, the plurality of metabolite data each corresponding to a respective amount of a plurality of metabolites generated by culturing a cell line for producing the antibody, the culture parameter being detected from the cell line in culture; acquiring of a degree of relevance between the culture parameter and each of the plurality of metabolites on the basis of the time-series data; and generating of display data based on the degree of relevance.
With such a configuration, the display data based on the degree of relevance is generated. Therefore, the manufacturer can presume a culture condition to be adjusted by viewing an image based on the display data, and as a result, it is possible to assist production of the antibody.
The embodiments disclosed herein should be considered as being illustrative examples and not limitations in any sense. The scope of the present disclosure is indicated by the scope of the claims rather than the above description of the embodiments, and is intended to include all modifications within meanings and a scope equivalent to the scope of the claims.
1 assisting system; 2 culture device; 3 culture condition; 4 sensor group; 6 analysis device; 10 first culture device; 30 display device; 30A display region; 40 input device; 48 name image; 50 network; 100 information processing device; 102 input unit; 104 request unit; 106 display control unit; 162 ROM; 164 RAM; 200 computing device
Number | Date | Country | Kind |
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2021-081516 | May 2021 | JP | national |
Filing Document | Filing Date | Country | Kind |
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PCT/JP2022/012559 | 3/18/2022 | WO |