Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier.
Such claim limitation(s) is/are:
“wherein data from the biological assay is obtained using analytical device” in claim 1, lines 4-5; and the analytical device that is recited again in line 16;
“one or more processors that….are configured to…” in claim 1, line 15;
“wherein data from the biological assay is obtained using an analytical device” in claim 2, lines 4-5; and the analytical device that is recited again in line 13;
“the one or more processors are further configured to…” in claim 6, line 2;
“a thermal cycler block adapted to receive…” in claim 14, section (a);
“a detection device capable of detecting luminescence in claim 14, section (b);
“a thermal top-heat assembly adapted to….” In claim 14, section (c).
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
Regarding an “analytical device”, recited in claim 1, lines 4-5 and 16, Examiner notes that the analytical device is not recited as part of the claimed system. However, the claimed system is recited as being capable of obtaining data using an analytical device (see claim 1, lines 4-5), and thus the analytical device requires an interpretation.
An analytical device is interpreted to encompass the analytical devices as disclosed by Applicant
in paragraph 0102, and their equivalents [para. 0102: (a) a thermal cycler block adapted to receive a multi-well plate; (b) a detection device capable of detecting luminescence; and (c) a thermal top-heat assembly adapted to maintain even heating across the top of the multi well plate and to allow a luminescent signal to pass through to the detection device]; and
in paragraphs 0103 and 0183 and 0218, and their equivalents [paras. 0103, 0183, and 0218: a thermal cycler; thermal cyclers that comprise, consist of, or consist essentially of a thermal block adapted to receive samples or multi-well sample plates].
A detection device is interpreted to encompass detection devices as disclosed by Applicant such as in paragraph 0104 and their equivalences [para. 0104: CCD or CMOS sensor, CCD camera].
A processor is interpreted to encompass processors as disclosed by Applicant in paragraph 0142, and their equivalents [para. 0142: a single-threaded processor, a multi-threaded processor, a vector processor or parallel processor that implements a single-instruction, multiple data (SIMD) architecture].
A thermal cycler is interpreted to encompass a thermal cycler as disclosed by Applicant in paragraph 0103 [a thermal block].
A thermal top-heat assembly is disclosed in Applicant’s specification in paragraph 0102 as being “adapted to maintain even heating across the top of the multi well plate and to allow a luminescent signal to pass through to the detection device”. However, no structural details are disclosed [and one skilled in the art would not be able to ascertain the meaning of “thermal top-heat assembly”; see 112b rejection below.)
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-16 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
A)
Claim 1 recites “a desired activity” in lines 3-4.
Claim 1 also recites “the desired activity” in subsection f).
Claim 2, also recites “a desired activity” in lines 3-4.
Claim 2, also recites “the desired activity” in subsection f).
The limitation “desired activity” is indefinite since it is a limitation that is defined by reference to an object (or subject), and the relationship between the limitation and the object is not sufficiently defined.
For further explanation, see MPEP 2173.05(b), under the subheading “II. REFERENCE TO AN OBJECT THAT IS VARIABLE MAY RENDER A CLAIM INDEFINITE”, a portion of which is provided hereby below.
A claim may be rendered indefinite when a limitation of the claim is defined by reference to an object and the relationship between the limitation and the object is not sufficiently defined. That is, where the elements of a claim have two or more plausible constructions such that the examiner cannot readily ascertain positional relationship of the elements, the claim may be rendered indefinite. See, e.g., Ex parte Miyazaki, 89 USPQ2d 1207 (Bd. Pat. App. & Inter. 2008) (precedential) and Ex parte Brummer, 12 USPQ2d 1653 (Bd. Pat. App. & Inter. 1989). In Miyazaki, the Board held that claims to a large printer were not sufficiently definite because:
The language of claim 1 attempts to claim the height of the paper feeding unit in relation to a user of a specific height who is performing operations on the printer.... Claim 1 fails to specify, however, a positional relationship of the user and the printer to each other.
Miyazaki, 89 USPQ2d at 1212. In Brummer, the Board held that a limitation in a claim to a bicycle that recited “said front and rear wheels so spaced as to give a wheelbase that is between 58 percent and 75 percent of the height of the rider that the bicycle was designed for” was indefinite because the relationship of parts was not based on any known standard for sizing a bicycle to a rider, but on a rider of unspecified build. Brummer, 12 USPQ2d at 1655.
In the present case, the limitation “the desired activity” is indefinite since it is a limitation that is defined by reference to an object (or subject), and the relationship between the limitation and the object is not sufficiently defined.
Examiner notes that what is considered “desired” appears to depend on a determination or predetermination based on an unspecified object (e.g., a setting or programming) or a subject (e.g., a user or other person), rather than any known standard, and the relationship between the limitation and the object is not sufficiently defined. Therefore the present limitation is indefinite for reasons analogous to that set forth in Miyazaki, where the limitation is indefinite because the claim recites the height of the paper feeding unit in relation to a user of a specific height who is performing operations on the printer though fails to specify a positional relationship of the user and the printer to each other. The present limitation is also analogous to Brummer, where the limitation is indefinite because the relationship of parts was not based on any known standard for sizing a bicycle to a rider, but on a rider of unspecified build.
Moreover, Applicant’s specification does not provide clarity to the limitation “desired activity”. The specification gives some examples of “desired activity” but does not provide a definition. While the claims are read in light of the specification, the disclosures in the specification are not read into the claims unless they provide a clear definition to a limitation in the claim.
The following are excerpts from Applicant’s specification (as provided in the US PreGrant Publication 20250130234) which disclose various examples of what can be considered a “desired activity”. These excerpts demonstrate that the meaning of “desired activity” can depend on factors that can vary in a way that renders the meaning of “desired activity” indefinite in a claim.
“In aspects, the disclosed methods for data analysis determine whether the analyte has desired activity in the biological system. The “desired activity” may be any property of the analyte that impacts or alters the functioning of the biological system, as informed by the underlying biology of the system. Examples include wherein the analyte is a ligand that binds to a target protein, wherein the analyte facilitates the targeting of particular cells, wherein the analyte inhibits the functioning of a target enzyme, and wherein the analyte alters the expression of a target gene. Those skilled in the art will readily understand the desired activity will be context dependent based on the nature of the biological assay, the biological system and th” para. e methods used for data collection. Those skilled in the art will further understand that whether an activity is “desired” will depend on the nature of the system under investigation. For example, a small molecule ligand's activity inhibiting a protein may be desirable in some contexts and undesirable in others. Those skilled in the art will be readily able to identify the appropriate activity for the purposes of the disclosed analytical methods based on biological and technological context.” Para. 0112 (emphasis added).
“In aspects of the disclosure where the biological assay generating data for analysis is RT-CETSA, the RT-CETSA assay may be used as a way of elucidating binding (or lack thereof) between the target protein of interest and the analyte in living cells. Accordingly, the “desired activity” may be the ability of the analyte to bind to a target protein. Such binding may result in a thermal stabilizing effect that can be detected by analyzing the data from an RT-CETSA assay according to the disclosed methods.” Para. 0113 (emphasis).
“Aspects of the disclosure comprise the use of a first model, wherein the model is a linear model. In aspects, this model is constrained to slope=0, and may be referred to as a null model. The null model assumes that the analyte does not have the “desired activity” in the biological system. For example, in the context of RT-CETSA, the null model assumes that there is no thermal stabilizing effect caused by the analyte binding to the target of interest.” Para. 0124 (emphasis added).
“According to aspects of the disclosure, the analyte is determined to have the desired activity in the biological system if the Mann-Whitney U test indicates that the second model is a better fit at a given value of the first independent variable than the first (null) model at one or more of the tested values of the first independent variable. For example, in the analysis of RT-CETSA data, an analyte will be identified as having the desired activity if, at one or more temperatures, the log logistic model is a better fit than the null model based on the Mann-Whitney U test. In aspects the log-logistic model may be a better fit across multiple temperature points along the gradient.” Para. 0129 (emphasis added).
“At step 812, the system analyzes the results of the goodness of fit test to determine whether the analyte has the desired activity by determining whether the second model is a better fit than the first model at one or more tested values for the first independent variable. According to aspects of the disclosure, the analyte is determined to have the desired activity in the biological system if the Mann-Whitney U test indicates that the second model is a better fit at a given value of the first independent variable than the first (null) model at one or more of the tested values of the first independent variable. For example, in the analysis of RT-CETSA data, an analyte will be identified as having the desired activity if, at one or more temperatures, the log logistic model is a better fit than the null model based on the Mann-Whitney U test.” Para. 0137 (emphasis added).
“At step 814, responsive to determining for the single analyte that the second model is a better fit than the first model based on the analysis using the non-parametric goodness of fit test, identify the single analyte as having desired activity in the biological system. For example, an analyte may be identified as having the desired activity, if at one more value for the first independent variable, the concentration response data for the analyte better fits the log logistic model than the null model. For example, in the context of RT-CETSA an analyte may be identified as having the desired activity if the results for at least one temperature point fit the log logistic model better than the null model. In addition, following step 814, the system and method can involve calculating EC.sub.50 of the analyte at temperature corresponding to the maximal RSS value, which is not explicitly depicted in FIG. 8.” Para. 0138 (emphasis added).
“At step 816, responsive to a determination that the second model is not a better fit based on the non-parametric goodness of fit test, the system identifies the analyte as not having the desired activity in the biological system. In aspects wherein the biological assay is RT-CETSA, an analyte may be identified as not having the desired activity where the null model is a better fit across the temperature gradient.” Para. 0139 (emphasis added).
In summary, these excerpts demonstrate that the meaning of “desired activity” can depend on factors that can vary in a way that renders the meaning of “desired activity” indefinite in a claim. What is considered “desired” appears to depend on a determination or predetermination based on an unspecified object (e.g., a setting or programming) or a subject (e.g., a user or other person), rather than any known standard, and the relationship between the limitation and the object is not sufficiently defined.
B)
Claim 14, section (c) recites “a thermal top-heat assembly adapted to….”
A thermal top-heat assembly is disclosed in Applicant’s specification in paragraph 0102 as being “adapted to maintain even heating across the top of the multi well plate and to allow a luminescent signal to pass through to the detection device”. However, no structural details are disclosed, and one skilled in the art would not be able to ascertain the meaning of “thermal top-heat assembly”.
C)
Claim 3, recites “wherein the non-parametric goodness of fit test is a Mann-Whitney U test”. Examiner notes that the specification discloses the following in paragraph 0128:
“The RSS values for both models are then compared at each value for the first independent variable using a non-parametric goodness-of-fit test, for example a Mann-Whitney U non-parametric test. The Mann-Whitney U non-parametric test will be familiar to those skilled in the art.”
However, Examiner finds that a Mann-Whitney U non-parametric test does not appear to be sufficiently well-known such that one of ordinary skill in the art would be reasonably apprised of the scope of the invention.
Moreover, the Mann-Whitney U non-parametric test appears to be a trademark/trade name. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a non-parametric goodness of fit test and, accordingly, the identification/description is indefinite.
D)
Claim 8 recites in line 2: “small molecules”.
Examiner notes that Applicant’s specification in paragraph 0099 discloses the following.
“Aspects of the method further comprise contacting the protein construct with one or more analytes or additional test molecules. In such aspects, the RT-CETSA assay may be used to detect binding (or lack thereof) between the target protein of interest and the test analyte in the cells. The analyte may be a small molecule. In aspects, the analyte binds to the target protein of interest. Examples of suitable small molecules include, without limitation, potential drug candidates, ligands known to bind to the target protein(s) of interest, known inhibitors of the target protein(s) of interest, and molecules with unknown biological activity.” Para. 0099 (emphasis added).
While Applicant in paragraph 0099 gives examples of small molecules, this disclosure merely gives examples, rather than a definition. In any case, the examples in paragraph 0099 encompass an exhaustive number of molecules that can be relatively large, and are too generic to be considered a definition of “small molecule”. While the term “small molecule” may have been often used by one skilled in the art, there may be various understandings of what constitutes a “small molecule”. Examiner notes that the term “small molecule” in the art can be a molecule that has a low molecular weight that is ≤ 1000 daltons, or ≤ 900 daltons, or ≤ 800 daltons, and it is not clear as to what Applicant means by “small molecule” or what molecular weight is considered “small” by Applicant. Clarification is requested.
E)
Similarly, claim 9 recites “large molecules”. There is no definition or example in Applicant’s specification as to what is considered to be large molecules, and there is insufficient disclosure in Applicant’s specification for one skilled in the art to ascertain a clear meaning of “large molecules”.
Clarification is requested.
F)
Claim 12 recites “high throughput screening”. The term “high” or “high throughput screening” a relative term which renders the claim indefinite. The terms are not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. For examination purposes, “wherein the analytical device is configured for high throughput screening” is interpreted to encompass any analytical device that is configured for screening.
G)
Claims 1 and 2 each recite in the preamble, “wherein the biological assay comprises Real-Time Cellular Thermal Shift Assay (RT-CETSA), differential scanning fluorimetry, thermal shift analysis, intrinsic fluorescence differential scanning fluorimetry, or nano differential scanning fluorimetry (nanoDSF)”.
It is not clear whether or not these types of assays are required by the claims, since they are not recited in the body of the claim. Examiner notes that the assay is recited in the preamble of claims 1 and 2, and the body of the claims relate to receiving results from the device that performed the assay.
However, the device of claim 1 does not comprise the analytical device, but rather comprises a system that is capable of using results received from the analytical device. Similarly, the method of claim 2 does not comprise use of the analytical device, but rather it comprises use of the results from the analytical device—see subsection (a) of claims 1 and 2, respectively. For examination purposes, this will be the interpretation. However, it is not entirely clear if this is the intention by Applicant, since the recited assays and the analytical device are not recited as part of the device of claim 1 nor method of claim 2. Likewise, regarding claim 13, which recites “wherein the biological assay is RT-CETSA” refers to the assay in the preamble of claim 2 (from which claim 13) depends, and the assay is not part of the method of claim 2 (or its dependent claim 13). Examiner notes that claims 2 and 13 is directed to a method of using the results of the assay provided by the analytical device, but does not require the assay or analytical device. Reciting specific assays in the preamble of claim 2 without requiring the assay anywhere in the body of claim 2 makes it unclear if the specific assays are required by claim 2.
Likewise, while claim 13 recites the assay (and specifically the assay RT-CETSA) in the body of the claim, claim 13 does not positively require the assay since it merely refers to the assay recited in the preamble of claim 2 [rather than positively reciting the assay, such as –wherein the method further includes performing an assay that is RT-CETSA--].
Clarification is required to make clear whether or not the assay, or analytical device, or the specific assays such as RT-CETSA are required by the claims.
The remaining claims are rejected since they depend from one of the claims above without clarifying the vagueness.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The claim(s) recite(s) the following, which are each an abstract idea (which encompasses a mental step) and is therefore a judicial exception:
a memory storing instructions;
(b) processing the initial results to obtain processed results;
(d) determine a plurality of residual sum of squares (RSS) values for the first and second models at each tested value of the first independent variable;
(e) analyzing the plurality of RSS values using a non-parametric goodness of fit test at each tested value of the first independent variable;
(f) responsive to determining for the single analyte that the second model is a better fit than the first model for at least one tested value of the first independent variable, identify the single analyte as having the desired activity in the biological system.
Moreover, the claims recite the following which is based on a mathematical concept, i.e., a natural law:
(c) fit the processed results for each concentration of a single analyte to a first model and a second model at each tested value of the first independent variable, wherein the first model is a linear null model with a slope of 0, and the second model is an alternative logarithmic model
(e) analyze the plurality of RSS values using a non-parametric goodness of fit test at each tested value of the first independent variable.
These judicial exceptions are not integrated into a practical application because none of the methods of claims 1-16 recite a practical application nor include additional elements that are sufficient to amount to significantly more than the judicial exception, as the remaining limitation of independent claims 1 and 2, is subsection (a), which recites “receive initial results from the analytical device” is merely data gathering, i.e., an extra-solution activity, which is neither a practice application, nor elements that are sufficient to amount to significantly more than the judicial exception. Moreover, steps (b) through (e), as well as step (g), which recites repeating steps (c)-(f), are directed to the judicial exceptions themselves (an abstract idea or mathematical concept), as noted further above, and therefore cannot amount to a practical application nor an element that is sufficient to amount to significantly more than the judicial exception.
Examiner notes that “analytical device” (in the preamble of claims 1 and 2, respectively) and “one or more processors” (in the body of claims 1 and 2) are recited at a high level of generality and therefore do not amount to more than a well-known, conventional, and routine analytical device and processor.
The remaining claims also do not recite a practical application nor elements that are sufficient to amount to significantly more than the judicial exception, for the following reasons.
Regarding claim 3, the non-parametric goodness of fit test is directed to a mathematical concept (a judicial exception itself).
Regarding claims 4 and 5, the log-logistic fit model is directed to a mathematical concept (a judicial exception itself).
Regarding claim 6, which recites “wherein the one or more processors are further configured to calculate an EC50 value for the single analyte by plotting the RSS values from the first and second models at each value of the first independent variable, and then fitting the second model to the processed results at the value of the first independent variable where the amount of the RSS difference between the first and second models is greatest” (emphasis added), this claim is also directed to a mathematical concept (“calculate” and “fitting”), which is a judicial exception itself.
Regarding claims 7-11, these claims recite details regarding the analyte, which is recited as part of the intended use of the device of claim 1, or is recited as part of the data gathering in which the results are used by the method of claim 2. Neither an intended use of a system, nor data gathering of a method is considered to amount to a practical application or elements which are sufficient to amount to significantly more than the judicial exception.
Claim 12 recites that the analytical device is configured for high throughput screening, which is recited at a high level of generality and therefore do not amount to more than a well-known, conventional, and routine analytical device for screening.
As to claim 13, while there is lack of clarity as to whether or not the assay, or analytical device, or the specific assay RT-CETSA is required by the claims (see discussion above in subsection (G) in the rejection under 35 USC 112(b), for examination purposes, the assay, the analytical device, and specific assays recited, including the RT-CETSA (Real-Time Cellular Thermal Shift Assay) are interpreted as not part of the method of claim 2. The assay is recited in the preamble as the assay in which the results are provided to an analytical device, which is processed according to the method of claims 2 and 13. While claim 13 recites the assay (and specifically the assay RT-CETSA) in the body of the claim, claim 13 does not positively require the assay since it merely refers to the assay recited in the preamble of claim 2 [rather than positively reciting the assay, such as –wherein the method further includes performing an assay that is RT-CETSA--]. In other words, Applicant’s claim 2 is interpreted as a method that receives results from an analytical device (see step (a) etc.), and claim 13 is interpreted as a method that is capable of being performed using results from an RT-CETSA type of assay, and performing the recited steps with those results.
Because the RT-CETSA is not required in claim 13, the RT-CETSA cannot be considered a practical application or an element that is sufficient to amount to significantly more than the judicial exception.
Conclusion
No claims are allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Martinez et al., “A widely-applicable high throughput cellular thermal shift assay (CETSA) using split Nano Luciferase”, Scientific Reports, vol. 8, no. 1, 1 December 2018 page 9472 (cited in the IDS of 6/20/24). This references teaches: “Assessment of the interactions between a drug and its protein target in a physiologically relevant cellular environment constitutes a major challenge in the pre-clinical drug discovery space. The Cellular Thermal Shift Assay (CETSA) enables such an assessment by quantifying the changes in the thermal stability of proteins upon ligand binding in intact cells. Here, we present the development and validation of a homogeneous, standardized, target-independent, and high-throughput (384- and 1536- well formats) CETSA platform that uses a split Nano Luciferase approach (SplitLucCETSA). The broad applicability of the assay was demonstrated for diverse targets…” (See abstract.)
Henderson et al., “High-throughput cellular thermal shift assays in research and drug discovery”. 2020 Feb;25(2):137-147. doi: 10.1177/2472555219877183. This assay teaches: “Thermal shift assays (TSAs) can reveal changes in protein structure, due to a resultant change in protein thermal stability. Since proteins are often stabilized upon binding of ligand molecules, these assays can provide a readout for protein target engagement”. (See abstract).
US 20150160214. This reference discloses an apparatus and methods for measuring cell or platelet adhesion using a processor that calculates both a pause time and a roll time of platelets, (see abstract). Paragraph 0121 discloses that goodness of fit was calculated, and the residual sum of squares are individual observed and fit values at any given temperature is observable.
US 20220026446. This reference analysis of structured amyloidogenic nano-plaques using residual sum of squares (RSS) an zero-slope linear regression (para. 0422).
US 20020081232. This reference discloses in the abstract the following:
“C-hemical sensors for detecting the activity of a molecule or analyte of interest is provided. The chemical sensors comprise and array or plurality of chemically-sensitive resistors that are capable of interacting with the molecule of interest, wherein the interaction provides a resistance fingerprint. The fingerprint can be associated with a library of similar molecules of interest to determine the molecule's activity.”
This reference discloses the following in paragraph 0073:
“A quantitative measure of the predictive power of the QSAR can be obtained by building a model using the biological and sensor response data from all the molecules except one, and then predicting the activity of the excluded molecule with that model. The procedure is repeated for each molecule in the data set, and the predictive sum of squares (PRESS) is defined as the sum, over all analytes, of the squared differences between the predicted and actual biological activity. Using equation 3, the PRESS for the set of 20 alcohols is 0.221. This value can be compared to the residual sum of squares, RSS, in which one QSAR equation (fit to all samples) is used to calculate the predicted activity. As would be expected, the RSS of 0.117 is lower than the PRESS. More significantly, a large difference between the PRESS and RSS would imply that the model had used too many parameters and overfit the data, and this appears not to be the case.” Para. 0073 (emphasis added).
Examiner notes that these references are cited above but not relied upon because they do not disclose or fairly suggest a system comprising a processor that is configured to:
(c) fit processed results for each concentration of a single analyte to a first model and a second model at each tested value of a first independent variable, wherein the first model is a linear null model with a slope of 0, and the second model is an alternative logarithmic model;
(d) determine a plurality of residual sum of squares (RSS) values for the first and second models at each tested value of the first independent variable;
(e) analyze the plurality of RSS values using a non-parametric goodness of fit test at each tested value of the first independent variable;
(f) responsive to determining for the single analyte that the second model is a better fit than the first model for at least one tested value of the first independent variable, identify the single analyte as having the desired activity in the biological system.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Ann Montgomery whose telephone number is (571)272-0894. The examiner can normally be reached Mon-Fri, 9-5:30 PM PST.
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/Ann Montgomery/Primary Examiner, Art Unit 1678