DETAILED ACTION
The amendment and RCE filed on 11/21/2025 has been entered and fully considered. Claims 21-34 are pending, of which claim 21 is amended.
Response to Amendment
In response to amendment, the examiner establishes rejection under 112b, and maintains rejection over the prior art established in the previous Office action.
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 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.
Claim 21-34 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.
1. Internal Inconsistency in Scope of “biological sample”
The claim 21 recites:
“the biological sample is … animal whole blood, animal plasma, animal biological fluids, or a single cell organism”
A single-cell organism (e.g., yeast, bacteria, protozoa) is neither an animal nor a sub-type of animal biological fluid/tissue. The transitional structure “wherein the biological sample is … animal [X] … or a single cell organism” mixes animal-derived samples and non-animal whole organisms within one Markush group without providing boundaries for how the claimed workflow applies to fundamentally different sample types.
Thus, it is unclear whether the claim is directed to:
animal-derived biological samples,
single-cell organisms, or
both categories,
and whether all downstream processing steps (e.g., “complement of proteins,” “10–50 cells,” “at least one reactor vessel,” “less than 500 ng”) are intended to apply simultaneously to these divergent sample classes.
The metes and bounds of the claim are therefore unclear.
2. Indefinite Structural Limitation: “hydrophilic surfaces have a non-zero total surface area less than 25 mm²”
Claim 21 recites the phrase:
“hydrophilic surfaces have a non-zero total surface area less than 25 mm²”
is indefinite because:
The claim does not identify which portions of the reactor vessel are counted as “hydrophilic surfaces.” It is unclear whether the inner surface area only, the bottom, the walls, a coating, or an insert is intended to be included.
No test method is provided for determining surface area of hydrophilic microreactor surfaces at this small scale.
A POSITA cannot determine with reasonable certainty whether a given micro-reactor vessel falls inside or outside the claimed bounds.
3. Overlapping and Ambiguous Volume Limitations
The claim 21 simultaneously recites:
first volume < 1000 nL transferred into the reactor vessel
transferred processed sample < 50 μL
diluted sample ≥ 5 μL
But the step:
“diluting … comprises dispensing a volume of a wash solution into the at least one reactor vessel and subsequently transferring the at least one reactor vessel’s contents to the one well”
does not specify:
how many washes,
what volume(s) of wash solution,
whether all wash volumes are combined,
whether dilution occurs entirely in the well or partly in the vessel, and
whether the final diluted volume must include both the carrier buffer and the wash solution.
A POSITA cannot determine whether any implementation that achieves ≥5 µL diluted sample necessarily requires some minimum or maximum wash volume; thus, the scope of the claim is unclear.
4. Functional Language Without Structural Support: “can identify greater than 3,000 unique species from 10–50 cells”
The closing clause of claim 21:
“wherein the proteome analysis can identify greater than 3,000 unique species from 10-50 cells”
is an intended result not tied to:
any specific instrument performance parameters,
LC-MS settings,
run time,
chromatography format,
detector type, or
data-processing pipeline.
This result clause does not modify or structurally limit any of the preceding steps and instead imposes an indefinite performance requirement on the entire system.
Two implementations performing the exact same steps may or may not meet the “>3,000 proteins” outcome depending on external factors (instrument model, detector sensitivity, software version, sample preparation efficiency).
Thus, the claim’s scope depends on variable, unclaimed factors, rendering the boundary between infringing and non-infringing embodiments indefinite.
5. Indefiniteness of Environmental Limitation: “performed under a relative humidity of 80% to 95%”
The claim 21 recites:
“are all performed under a relative humidity of 80% to 95%”
It is unclear:
whether the humidity applies to the air surrounding the platform,
the internal volume of the vessel,
the well plate,
the mass spectrometer interface, or
only the sample-handling steps but not the analytical step.
Humidity inside a mass spec inlet is typically tightly controlled and not reflective of the ambient lab humidity.
Thus, the scope of where humidity must be maintained is unclear, resulting in uncertainty regarding whether an accused process infringes.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim 21-27, 29-30 and 32 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ramsay et al. (US 2007/0004044) (Ramsay) in view of Dixon (AACC’s fifth annual Mass Spectrometry Conference, 2015), Garyantes (US 6,565,813) and Pugia et al. (WO 2015/184321) (Pugia).
Regarding claims 21, Ramsay teaches a method of proteome analysis comprising the steps of:
obtaining a biological sample, wherein the biological sample is an animal tissue sample, animal biopsy, animal cell homogenate, animal cell fraction, cultured animal cells, non-cultured animal cells, animal whole blood, animal plasma, animal biological fluids, or a single cell organism (par [0005] [0044]);
transferring a first volume of the biological sample to a platform, where the platform comprises a substrate comprising at least one reactor well, each well has a non-zero total surface area less than 25 mm2, and wherein transferring the first volume of the biological sample comprises transferring the first volume of the biological sample to the at least one reactor vessel, wherein the first volume is a non-zero amount less than 1000 nL (Fig. 1, par [0099]),
processing the biological sample in the at least one reactor well (par [0099]), wherein the processing comprises lysing, extraction and denaturation of proteins in the biological sample (par [0067][0068]);
extracting from at least one reactor well a processed sample comprising less than 500 ng of a complement of proteins, peptides related to the complement of proteins, or both (Fig. 1, par [0099][0104])
transferring the extracted sample from the one well to a mass-spectrometry based analytical instrument (par [0105]); and
providing protein identification for each of a plurality of proteins composing the complement of proteins (par [0113] [0121]).
Ramsay teaches that the plate is microtiter plate (par [0092]). Thus, it is more likely that each well of the microtiter plate has a non-zero total surface area less than 25 mm2 and contains less than 1000 nl or 500 ng proteins, and the volume of the processed sample that is transferred is less than 50 µL.
It is conventional to substitute well with vessel, because both vessel and well are designed for holding liquid. The result is predictable.
Ramsay teaches that “As mentioned, the porous support or sorbent material may be fixed or secured in its position in the well or vial by a fixing structure such as a retainer (indicated as (3) in FIG. 7).” (par [0067]). “The porous support comprising the liquid sorbent material mainly has two functions. The first is to embed the internal standards (reference material) as descibed below at predefined concentration ready for addition of the biological sample. The second is the immobilizing of the contents of each sample. This immobilizing step induces cell lysis, protein immobilisation/precipitation and salt and many other drug or metabolite retention from each of the samples” (par [0068]). Here, Ramsay teaches that wherein the processing comprises lysing (cell lysis), extraction (protein immobilization) and denaturation of proteins (protein precipitation) in the biological sample.
Ramsay does not specifically teach dispensing the processed sample into one well on a well plate having a plurality of wells, wherein the one well is pre-loaded with a volume of a liquid carrier buffer; and diluting the processed sample, thereby yielding in the one well a diluted sample, before transferring the diluted sample from the one well to a mass-spectrometry based analytical instrument. In the analogous art of sample preparation for mass-spectrometry, Dixon teaches diluting the processed biological sample, thereby yielding a diluted sample (page 11). Dixon teaches that “Dilution of prepared sample minimizes the presence of salts and matrix effects.” (page 11). Dixon teaches that the biological sample includes urine, oral fluid, plasma, serum, whole blood, meconium and tissue (page 5). At time before the filing, it would have been obvious to one of ordinary skill in the art to diluting the processed sample that is transferred in Ramsay with preloaded liquid carrier buffer in another well, wherein the diluted sample has a volume of at least 5 μL, in order to minimize the presence of salts and matrix effects. A person skilled in the art would have been motivated to do so, because the extracted proteins from a biological sample may contains matrix co-extractives and salt that can change the ionization efficiency of an analyte causing signal suppression or enhancement.
Ramsay does not specifically teach using a well plate having a plurality of wells for diluting the processed sample. However, Ramsay discloses a well plate having a plurality of wells for sample processing. Therefore, it would have been obvious to one of ordinary skill in the art to use a corresponding similar well plate for diluting the processed sample, in order to streamline analyzing multiple samples. The corresponding similar well plate can be a duplicated well plate.
Ramsay does not specifically teach the diluting comprises dispensing a volume of a wash solution into the one reactor vessel and subsequently transferring the one reactor vessel's contents to the one well. However, a person skilled in the art would have appreciated that dispensing a volume of a wash solution into the one reactor vessel and subsequently transferring the one reactor vessel's contents to another well , would transfer more complete content from the reactor to the another well.
The rationale to modify or combine the prior art does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, established scientific principles, or legal precedent established by prior case law. In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988); In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992). In this case, the technique of wash and transfer has been widely used in a kitchen or a lab to completely transfer liquid from one container to another container. It is a knowledge generally available to one of ordinary skill in the art.
Ramsay does not teach that wherein the platform comprises a substrate comprising at least one reactor vessel having one or more hydrophilic surfaces configured for containment of a biological sample, a spacer containing a spacer aperture, wherein the spacer aperture is dimensioned to surround the at least one reactor vessel when the spacer is positioned on the substrate, and a cover positioned on the spacer. However, Garyantes teaches a platform wherein the platform comprises a substrate comprising at least one reactor vessel having one or more hydrophilic surfaces configured for containment of a biological sample (col. 13, lines 26-29), a spacer containing a spacer aperture, wherein the spacer aperture is dimensioned to surround the at least one reactor vessel when the spacer is positioned on the substrate, and a cover positioned on the spacer (Fig. 6, col. 13, lines 24-37). Garyantes teaches that “Typically, the virtual wells are formed by an arrangement of relatively hydrophilic domains within relatively hydrophobic fields. Solvated samples (compounds) and assay reagents are confined to the more hydrophilic domains of the virtual wells by the edges of the more hydrophobic fields. The use of virtual wells allows one to run high throughput screening assays that require the capture and washing of an assay component prior to reading, as well as assays simply requiring the mixing of components and reading, with assay mixtures having volumes on the order of about 10 ml to 10 ul.” (col. 3, lines 21-31). And “Spacers can aid in moving two plates into close proximity. Generally, spacers separating two plates can be from 100 um to 4,000 um thick.” (col. 7, line 59-61). At time before the filling it would have been obvious to one of ordinary skill in the art to use a platform wherein the platform comprises a substrate comprising at least one reactor vessel having one or more hydrophilic surfaces configured for containment of a biological sample (col. 13, lines 26-29), a spacer containing an aperture, wherein the aperture is dimensioned to surround the at least one reactor vessel when the spacer is positioned on the substrate, and a cover positioned on the spacer, in order to confine sample in the well and create small volume well for high throughput screening assays.
Ramsay does not specifically teach that wherein transferring the diluted sample comprises collecting the diluted sample in a capillary and coupling the capillary to the mass-spectrometry-based analytical instrument. However, Pugia teaches collecting a sample in a capillary (par [0050]). Thus, it would have been obvious to one of ordinary skill in the art to select capillary for collecting the diluted sample in a capillary and coupling the capillary to the mass-spectrometry-based analytical instrument, because the selection is based on its suitability for the intended use.
Ramsay does not specifically teach that wherein the transferring the first volume of the biological sample to the platform, processing the biological sample in the at least one reactor vessel, extracting from the at least one reactor vessel the processed sample, dispensing the processed sample into one well on the well plate having a plurality of wells, and diluting the processed sample, are all performed under a relative humidity of 80% to 95%. However, Garyantes teaches that “Since plates containing virtual wells are open only during the brief period while sample or reagents are being dispensed, there is little evaporation associated with their use. Evaporation can be further minimized by cooling plates to the dew point during dispensing. This method of controlling evaporation is advantageous compared to traditional methods such as increasing the humidity because it is less damaging to the instrumentation and stabilizes fragile reagents during the dispense.” (col. 19, lines 32-40). Here, Garyantes teaches two methods to reduce the sample evaporation. 1. Cooling the sample plates to dew point, so that the relative humidity at the sample plates is close to 100%. 2. Traditional method, increasing the relative humidity of the environment of the sample plates close to 100%. Thus, it would have been obvious to one of ordinary skill in the art to increase the relative humidity of the environment of the sample plates to 80% to 95%, in order to reduce the sample evaporation.
The claimed “>3,000 proteins from 10–50 cells” is a performance result, not a structural limitation, and is an expected outcome of combining known micro-volume proteomic workflows aimed at maximizing recovery and sensitivity.
It is the inherent result of using nanoliter micro-reactors (Garyantes), high-recovery prep (Dixon), low-cell workflows (Pugia), and MS analysis (Ramsay)
As written, the limitation merely states a desired analytical outcome dependent on:
instrument model and sensitivity,
acquisition parameters,
chromatography configuration,
data-processing software,
ion statistics,
operator settings, and
sample type.
Such performance results do not confer patentable distinction unless the claim includes specific steps or structures that mandatorily achieve that outcome. Claim 21 does not.
Regarding claim 22, Ramsay teaches using LC-MS to analyze the processed sample (par [0113]). Pugia teaches using capillary to collect the sample. Thus, it would have been obvious to one of ordinary skill in the art to couple the sample containing capillary to the head of the liquid chromatography column for LC-MS analysis.
Regarding claim 23, Microextraction columns are used in sample preparation to extract target compounds from a sample matrix. Thus, it would have been obvious to one of ordinary skill in the art to couple the sample containing capillary to a solid-phase microextraction column for further purification before LC-MS analysis.
Regarding claim 24, six months is a long time for processed sample storage. It is more likely that wherein the diluted sample is stored in the capillary for less than six months prior to coupling the capillary to the mass-spectrometry-based analytical instrument.
Regarding claim 25, twelve-month storage of biological sample is common.
Regarding claim 26, it would have been obvious to one of ordinary skill in the art to co-registering a spatial region of a tissue sample with a reactor vessel, and with a well, in order to track the process.
Regarding claim 27, Ramsay teaches that wherein the liquid carrier buffer comprises a mass spectrometry-compatible surfactant (par [0075]).
Regarding claim 29, Ramsay teaches that wherein the plurality of proteins comprises at least 1000 proteins (par [0113]).
Regarding claim 30, A person skilled in the art would have appreciate repeatedly dispensing a volume of a wash solution into the one reactor vessel and subsequently transferring the one reactor vessel's contents to the one well, would transfer more complete content from the reactor to the well.
Regarding claims 32, since the well in Ramsay has dimension in micrometer, it is more likely that the biological sample that the well is less than 100 nL, and the volume of the liquid carrier buffer is less than 50 μL.
Claim 28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ramsay in view of Dixon, Garyantes (US 6,565,813) and Pugia as applied to claim 21 above, and further in view of Chang et al. (Journal of Proteome Research, 2015) (Chang).
Regarding claim 28, Ramsay does not specifically teach that wherein the MS-compatible surfactant comprises ProteaseMAX, RapiGest, PPS Silent Surfactant, oxtyl β-D-glucopyranoside, n- dodecyl β-D-maltoside (DDM), digitonin, Span 80, Span 20, sodium deoxycholate, or a combination thereof. However, Chang teaches that wherein the MS-compatible surfactant comprises ProteaseMAX, RapiGest, PPS Silent Surfactant, oxtyl β-D-glucopyranoside, n- dodecyl β-D-maltoside (DDM) and digitonin (page 1588, par 2). At time of the invention it would have been obvious to one of ordinary skill in the art to select ProteaseMAX, RapiGest, PPS Silent Surfactant, oxtyl β-D-glucopyranoside, n- dodecyl β-D-maltoside (DDM), digitonin as the MS-compatible surfactant, because the selection is based on its suitability for the intended use.
Claim 31 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ramsay in view of Dixon, Garyantes (US 6,565,813) and Pugia as applied to claim 21-27, 29-30 and 32 above, and further in view of Cunanan et al. (US 2006/0154230) (Cunanan).
Regarding claim 31, Ramsay does not specifically teach that wherein the liquid carrier buffer is phosphate buffered saline, ammonium bicarbonate, tris(hydroxymethyl)aminomethane, liquid chromatography mobile phase, or a combination thereof. However, Cunanan teaches using phosphate-buffered saline as a buffer for storing biological tissue (par [0009]). Ramsay teaches that the biological sample include tissue (par [0044]). Thus, at time of the filing it would have been obvious to one of ordinary skill in the art to select phosphate buffered saline as the buffer for biological sample, because the selection is based on its suitability for the intended use.
Claim 33 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ramsay in view of Dixon, Garyantes (US 6,565,813) and Pugia as applied to claim 21-27, 29-30 and 32 above, and further in view of Morrogh et al. (BioTechniques, 2007) (Morrogh).
Regarding claim 33, Ramsay teaches that wherein the biological sample is an animal tissue sample (par [0045]).
Ramsay does not specifically teach that obtaining the animal tissue sample comprises laser-capture microdissection. However, Morrogh teaches that obtaining the animal tissue sample comprises laser-capture microdissection (page 41, par 1). Morrogh teaches that “The application of laser capture microdissection (LCM) technology to facilitate selective sampling of individual cells or groups of cells from histological specimens is gaining popularity and is now an established method of procuring cells for many downstream RNA, DNA, and protein experiments (1–7).” (page 41, par 1). At time before the filing it would ahe been obvious to one of ordinary skill in the art to select laser-capture microdissection for obtaining the animal tissue sample, because the selection is based on its suitability for the intended use.
Claim 34 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ramsay in view of Dixon, Garyantes (US 6,565,813) and Pugia as applied to claim 21-27, 29-30 and 32 above, and further in view of Thurman et al. (US 2011/0272405) (Thurman).
Regarding claim 34, Garyantes teaches that wherein the substrate comprising plurality of reactor vessels (col. 13, lines 26-29), and a spacer containing a spacer aperture, wherein the spacer aperture is dimensioned to surround the plurality of reactor vessels, and a cover positioned on the spacer (Fig. 6, col. 13, lines 24-37).
Garyantes does not specifically teach a membrane interposed between the spacer and the cover. However, Thurman teaches a sealing membrane (42) interposed between the two surfaces and seals the interface (Fig. 5, par [0040]). Thus, it would have been obvious to one of ordinary skill in the art to place a sealing membrane interposed between the spacer and the cover, in order to seal the interface. Since Garyantes teaches that the spacer has a spacer aperture wherein the spacer aperture is dimensioned to surround the at least one reactor vessel when the spacer is positioned on the substrate (Fig. 6, col. 13, 24-37), it would have been obvious to one of ordinary skill in the art to let the seal membrane fit the dimension of the spacer and having the same dimensioned aperture to surround the at least one reactor vessel when the membrane is positioned on the spacer, in order to seal the surface between the spacer and the cover.
Response to Arguments
Applicant's arguments filed 11/21/2025 have been fully considered but they are not persuasive.
1. Applicant’s reliance on the “>3,000 proteins from 10–50 cells” recital is not persuasive
Applicant amended Claim 21 to include:
“wherein the proteome analysis can identify greater than 3,000 unique species from 10–50 cells”
and argues that none of the cited references disclose such a feature, and therefore the §103 rejection should be withdrawn.
However:
(A) The newly added limitation in claim 21 is an intended result / performance outcome, not a structural or methodological limitation
The recited capability-MS identification of >3,000 proteins from 10-50 cells does not impose any specific structural, chemical, or operational steps beyond those already recited in the claim. As written, the limitation merely states a desired analytical outcome dependent on:
instrument model and sensitivity,
acquisition parameters,
chromatography configuration,
data-processing software,
ion statistics,
operator settings, and
sample type.
Such performance results do not confer patentable distinction unless the claim includes specific steps or structures that mandatorily achieve that outcome. Claim 21 does not.
(B) The prior art combination teaches the underlying features that reasonably achieve high-depth proteome coverage
As explained in the Final Rejection:
Ramsay teaches micro-aliquot sample preparation and MS workflows.
Dixon teaches micro-volume proteomic sample preparation, including low-ng peptide/protein loading appropriate for high-depth coverage.
Garyantes teaches hydrophilic micro-reactors <25 mm² and high-humidity handling of nanoliter volumes features expressly designed to prevent sample loss and enable very small-cell-count proteomic workflows.
Pugia teaches rare-cell and low-copy-number molecular analysis, including nanoliter-scale processing and capillary transfer to MS.
These references collectively teach methods directed to minimizing sample loss, maximizing recovery, and enabling nanoscale MS workflows aimed at highly sensitive proteome detection.
A POSITA would reasonably expect that these combined teachings enable deep proteome coverage, including coverage numerically exceeding 3,000 proteins in low-cell-count samples, because such coverage is a predictable function of:
sample preservation (Garyantes humidity + hydrophilic confinement),
efficient extraction of all proteins (Ramsay, Dixon),
minimized losses in nanoliter reactors (Garyantes),
and highly sensitive MS with capillary introduction (Pugia).
Thus, the newly added numerical result is a mere outcome of the obvious combination of prior-art sample preparation and MS methodologies.
(C) A claimed result is obvious if the underlying method is obvious
Even if the prior art does not explicitly quantify “3,000 proteins,” the Federal Circuit has long held that:
“Discovery of an optimum value of a result-effective variable is ordinarily within the skill of the art.”
“An otherwise obvious process does not become nonobvious simply because it yields improved results.”
The ability to increase proteome depth by reducing sample loss, increasing recovery, and applying sensitive MS is a routine optimization of the type expressly taught in Dixon and Pugia. The claimed numerical threshold represents an expected improvement, not an inventive step.
Applicant even states in the Remarks (page 5):
“This is an expected level of proteome coverage.”
This admission directly supports the Examiner’s position that the newly added number does not render the method nonobvious.
(D) Applicant’s specification cannot supply missing novelty
Applicant quotes internal paragraph [000145] to show that the claimed result is achievable.
However, the specification cannot be used as evidence that the prior art lacks the capability, and the fact that Applicant achieved a certain level of performance using an arrangement of known sample-prep tools does not establish nonobviousness unless the claim recites the specific means that produced that performance.
Claim 21 does not recite such specific means.
2. The art of record provides explicit motivation to combine
Each reference addresses sample handling at extremely small volumes and MS sensitivity limitations, providing strong motivation to combine their teachings:
Garyantes addresses evaporation and sample loss in nanoliter reactors.
Dixon addresses matrix suppression, recovery, and precision in micro-prep proteomics.
Pugia addresses rare-cell and low-abundance workflows and nanoliter MS introduction.
Ramsay provides the overall MS workflow integrated with small-volume extraction.
The combination solves well-known problems in small-cell proteomics using well-understood techniques. KSR requires no explicit suggestion when the improvement is predictable.
3. Claim 21 remains obvious over Ramsay + Dixon + Garyantes + Pugia
The amendment does not add a structural, transformative, or non-obvious operational step.
It merely adds a statistical outcome that flows naturally from the obvious combination of:
nanoliter confinement (Garyantes),
high-recovery proteomic prep (Dixon),
rare-cell/small-sample MS workflows (Pugia), and
established LC/MS sample workflows (Ramsay).
Therefore, the arguments do not overcome the §103 rejection.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to XIAOYUN R XU, Ph. D. whose telephone number is (571)270-5560. The examiner can normally be reached M-F 8am-5pm.
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/XIAOYUN R XU, Ph.D./Primary Examiner, Art Unit 1797