Ex Parte 6831994 et al

Patent Trial and Appeal Board

Feb 26, 2013

95000529 (P.T.A.B. Feb. 26, 2013)

UNITED STATES PATENT AND TRADEMARKOFFICE
UNITED STATES DEPARTMENT OF COMMERCE
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APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
95/000,529 02/19/2010 6831994 048522-0003 8420
22922 7590 02/26/2013
REINHART BOERNER VAN DEUREN S.C.
ATTN: AMANDA RUTTER, PARALEGAL
1000 NORTH WATER STREET
SUITE 2100
MILWAUKEE, WI 53202
EXAMINER
LEUNG, CHRISTINA Y
ART UNIT PAPER NUMBER
3992
MAIL DATE DELIVERY MODE
02/26/2013 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Illumina, Inc.
(Patent Owner and Appellant)

v.

Life Technologies Corporation
(Requester and Cross-Appellant)
____________

Appeal 2012-010385
Reexamination Control No. 95/000,529
US Patent 6,831,994 B2
Technology Center 3900
____________

Before RICHARD M. LEBOVITZ, JEFFREY B. ROBERTSON, and
RAE LYNN P. GUEST, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL

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This is a decision on appeal in an inter partes reexamination of U.S.
6,831,994 B2. The Patent Owner appeals the Examiner’s decision to reject
claims as anticipated and obvious. The Third Party Requester cross-appeals
the Examiner’s determination not to adopt rejections of claims as obvious
and the Examiner’s withdrawal of the rejection for impermissibly
broadening the scope of the claims. The Board’s jurisdiction for this appeal
is under 35 U.S.C. §§ 6(b), 134, and 315. We reverse and enter new grounds
of rejection.

STATEMENT OF THE CASE
The patent in dispute in this appeal is U.S. Patent No. 6,831,994 B2,
issued December 14, 2004 (hereinafter, “the ‘994 patent”). The Patent
Owner and Real Party in Interest is Illumina, Inc. (“Illumina”). Illumina’s
Appeal Brief 2, September 13, 2011 (“Illumina Appeal Br.”).
A replacement request for inter partes reexamination of the ‘994
Patent was filed on February 19, 2010 by a Third-Party Requester under 35
U.S.C. §§ 311-318 and 37 C.F.R. §§ 1.902-1.997. Request for Inter Partes
Reexamination 1. The Third-Party Requester is Life Technologies
Corporation (“Life”). Life Respondent Brief 1, October 12, 2011 (“Life
Resp’t Br.”).
The ‘994 patent was the subject of litigation in Life Technologies
Corp. v. Illumina, Inc., No.1:09-cv-00706-RK (D. Del., filed September 21,
2009). The Delaware Court issued a claim construction order on December
15, 2010. On April 6, 2011, the Delaware District Court ordered the transfer
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of the litigation to the Southern District of California, where the case is
designated 3:11-cv-00703-JAH-POR. Illumina Appeal Br. 2.
Related U.S. Patent 6,654,505 was subject of inter partes
reexamination, Application 95/001,292. An appeal was decided in that case.
Decision on Appeal in Appeal No. 2012-007309, mailed November 29,
2012.
In the present reexamination appeal, an oral hearing took place on
December 13, 2012. A transcript of the oral hearing was entered into the
record on January 24, 2013.
Claims
Claims 1-35 are pending. Claims 1-24, 26-30, and 33-34 stand
rejected by the Examiner. Claims 25, 31, and 35 are allowed by the
Examiner. Claim 32 is canceled. The rejections by the Examiner of claims
1-24, 26-30, and 33-34 are appealed by Illumina. Illumina App. Br. 5. Life
cross-appeals the Examiner’s determination not to adopt proposed rejections
of the claims. Life Technologies Appeal Brief 5, filed October 13, 2011
(“Life Appeal Br.”).
Claim 1 reads as follows (bracketed numerals added for reference to
the main limitations; underlining indicates amendments relative to the
original claims):
1. A system for detecting a sequence of optical signals from
each of a plurality of microparticles during a sequence of
processing steps, the system comprising:
[1] a planar array of uniformly sized spherical
microparticles, wherein the coefficient of variation of the
diameters of said microparticles is less than five percent;
[2] an optical train effective to collect and focus the
sequence of optical signals from the microparticles, and to
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record at least one optical characteristic of each microparticle
which can be used to determine the approximate center of said
microparticle;
[3] an imaging device onto which said signals are
focused, effective to generate and record a sequence of digital
images of the microparticles, with sufficient resolution for
individual microparticles to be distinguished; and
[4] signal tracking means effective to correlate the optical
signals from each of the microparticles in each of the sequence
of digital images with said center of said microparticle.

7. (Amended) The system of claim 1, wherein the system is
configured to designate a first pixel for determining
characteristics of an optical signal generated at a microparticle,
the first pixel being correlated with the center of the
microparticle.

APPEAL BY ILUMINA
Illumina appeals the following rejections by the Examiner (Illumina
Appeal Br. 5):
1. Rejection of claims 1-4, 6, 14-24, 26-30, and 33-34 under 35 U.S.C.
§ 102 as anticipated by Brenner;1
2. Rejection of claims 7-10 and 13 under 35 U.S.C. § 103 as obvious
over Brenner in view of Schmidt;2
3. Rejection of claims 7-10 and 13 under 35 U.S.C. § 103 as obvious
over Brenner in view of Gelles;3

1 Sydney Brenner, Molecular Tagging System, WO 96/12014 (published
April 25, 1996) (Brenner).
2 Christine E. Schmidt et al., Integrin-Cytoskeletal Interactions in Migrating
Fibroblasts are Dynamic, Asymmetric, and Regulated, J. Cell Biology,
123(4):977-991, 1993 (Schmidt).
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4. Rejection of claims 7-12 under 35 U.S.C. § 103 as obvious over
Brenner in view of Hicks;4 and
5. Rejection of claim 5 under 35 U.S.C. § 103 as obvious over
Brenner in view of Hansen.5

CLAIM INTERPRETATION
Limitation [4] of claim is in dispute in this appeal. We thus begin by
construing limitation [4] in view of the ‘994 patent specification.
The term “signal tracking means” is a means-plus-function term that
invokes 35 U.S.C. §112 ¶ 6. Its scope defined by the structure disclosed in
the specification plus any equivalents of that structure. See In re Donaldson,
16 F.3d 1189, 1195 (Fed. Cir. 1994) (en banc).
The ‘994 patent specification does not use the term “signal tracking
means.” However, it does describe the function of the signal tracking means
recited in the claim (“to correlate the optical signals from each of the
microparticles in each of the sequence of digital images with said center of
said microparticle”) and a structure which accomplishes the recited function.
As explained in the ‘994 patent specification and reflected in the
claims, optical signals are collected from the microparticles and used to

3 Jeff Gelles et al., Tracking kinesin-driven movements with nanometer-scale
precision, Nature, 331:450-453, 1988 (Gelles).
4 B.W. Hicks et al., Tracking Movements of Lipids and Thy1 Molecules in the
Plasmalemma of Living Fibroblasts by Fluorescent Video Microscopy with
Nanometer Scale Precision, J. Membrane Biology, 144(3):231-244, 1995
(Hicks).
5 W. Peter Hansen et al., Light Scatter-Based Immunoassay Without Particle
Self Aggregation, U.S. Pat 5,589,401 (granted December 31, 1996)
(Hansen).
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generate a sequence of digital images. This function is performed by the
imaging device [3] of claim 1. Once the optical signals are recorded in
successive digital images, the [4] signal tracking means performs the
function of correlating the optical signals from each of the microparticles in
each of the sequence of digital images with the center of the microparticle.

Findings of Fact
[FF1]6
The ‘994 patent specification describes a “detection means” with an
“important feature” of having the “ability to keep track of individual
microparticles through multiple process steps and/or cycles.” Col. 8, ll. 48-
50 (emphasis added).
[FF2]
The detection means (114) is shown in Figure 1a of the patent as
comprising a microscope, CCD (charge-coupled device which is capable of
generating a digital image), and computer. See col. 5, ll. 7-12; col. 8, ll. 48-
54.
[FF3]
In connection with the tracking, the ‘994 patent explains that the
“detection means (114) periodically records optical characteristics of
individual microparticles that provide a close approximation microparticle
centers.” Col. 8, ll. 51-54. This function appears to correspond to the
imaging device [3] of claim 1, such as the CDD device shown in Figure 1A
(FF2).

6 “FF” refers to a Finding of Fact.
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[FF4]
Once microparticle centers are determined, the patent describes
assigning pixels “for determining characteristics, e.g. intensity, of an optical
signal generated at each microparticle (602).” Col. 9, ll. 6-9.
[FF5]
The patent describes a preferred embodiment in which “initial pixel is
assigned which encloses the computed center of a microparticle.” Col. 9, ll.
24-26.
[FF6]
The ‘994 patent specification explains what structure performs the
pixel assignment (FF4 & FF5):
After the fluorescent image is collected, the focal plane of the
microscope objective is returned (814) to the microparticle
focal plane, where another image is collected (816) for the
purpose of computing microparticle centers as described above.
The image of microparticle centers is transferred to data
server (812) where data processor (818) assigns pixels of the
fluorescent image to each microparticle center, as described
above.
Col. 10, ll. 13-20 (emphasis added).
Analysis
The claimed correlation of the “the optical signals from each of the
microparticles in each of the sequence of digital images with said center of
said microparticle” is thus performed by the “data processor.” As the “data
processor” performs the computational function of assigning pixels of the
fluorescent images to the microparticle centers, it would be understood by
one of ordinary skill in the art to be a component of the computer shown in
Figure 1a (FF2).
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In cases involving a computer-implemented invention in which
the inventor has invoked means-plus-function claiming, [the
Federal Circuit] has consistently required that the structure
disclosed in the specification be more than simply a general
purpose computer or microprocessor.

That was the point made by this court in WMS Gaming, Inc. v.
International Game Technology, 184 F.3d 1339 (Fed. Cir.
1999). In that case, the court criticized the district court, which
had determined that the structure disclosed in the specification
to perform the claimed function was “an algorithm executed by
a computer.” The district court erred, this court held, “by failing
to limit the claim to the algorithm disclosed in the
specification.” Id. at 1348. The rationale for that decision is
equally applicable here: a general purpose computer
programmed to carry out a particular algorithm creates a “new
machine” because a general purpose computer “in effect
becomes a special purpose computer once it is programmed to
perform particular functions pursuant to instructions from
program software.” Id., quoting In re Alappat, 33 F.3d 1526,
1545 (Fed. Cir. 1994). The instructions of the software program
in effect “create a special purpose machine for carrying out the
particular algorithm.” WMS Gaming, 184 F.3d at 1348. Thus, in
a means-plus-function claim “in which the disclosed structure is
a computer, or microprocessor, programmed to carry out an
algorithm, the disclosed structure is not the general purpose
computer, but rather the special purpose computer programmed
to perform the disclosed algorithm.” Id. at 1349.
Aristocrat Technologies Australia Pty Ltd. v. International Game
Technology, 521 F3d 1328, 1333 (Fed. Cir. 2008).
It is thus made clear by Aristocrat that when a computer-implemented
invention is being claimed – as is the case here – the computer is not a
general purpose one, but rather a computer programmed to perform the
recited function, which in this case is “to correlate the optical signals from
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each of the microparticles in each of the sequence of digital images with said
center of said microparticle.” The claimed “signal tracking mean” is
therefore interpreted in light of the ‘994 patent specification to require a
computer, or equivalent data processing structure, which comprises software
or hardware that enables it to perform the claimed correlation function of
limitation [4].
The claim requires [3] an “imaging device” which “record[s]” digital
images and a [4] “signal tracking means” which correlates the digital images
with microparticle centers. The recordation of the image is therefore
explicitly recited in the claim to be carried out separately from the
subsequent correlation which is accomplished with the signal tracking
means. The correlation is performed in the ‘994 patent by a process
involving the assignment of pixels to the microparticle center (FF4-FF6).
However, we do not limit the claimed “correlate” limitation to this pixel
assignment process.

1. ANTICIPATION BY BRENNER
Claims 1-4, 6, 14-24, 26-30, 33, and 34 stand rejected under 35 U.S.C.
§ 102 as anticipated by Brenner. The issue is this rejection is as follows:
Does Brenner describe [4] “signal tracking means effective to
correlate the optical signals from each of the microparticles in each of the
sequence of digital images with said center of said microparticle”?
Findings of Fact
[FF7]
Typically, the sorted molecules are exposed to ligands for
binding, e.g. in drug development, or are subjected chemical or
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enzymatic processes, e.g. in polynucleotide sequencing. In both
of these uses it is often desirable to simultaneously observe
signals corresponding to such events or processes on large
numbers of microparticles.
Brenner, p. 25, ll. 34-38
[FF8]
Preferably, whenever light-generating signals, e.g.
chemiluminescent, fluorescent, or the like, are employed to
detect events or processes, loaded microparticles are spread on
a planar substrate, e.g. a glass slide, for examination with a
scanning system . . . . The scanning system should be able to
reproducibly scan the substrate and to define the positions of
each microparticle in a predetermined region by way of a
coordinate system. In polynucleotide sequencing applications,
it is important that the positional identification of
microparticles be repeatable in successive scan steps.
Brenner, p. 26, ll. 3-10 (emphasis added).
[FF9]
Such scanning systems may be constructed from commercially
available components, e.g. x-y translation table controlled by a
digital computer used with a detection system comprising one
or more photomultiplier tubes, or alternatively, a CCD array,
and appropriate optics, e.g. for exciting, collecting, and sorting
fluorescent signals . . . Computer software for table translation
and data collection functions can be provided by commercially
available laboratory software, such as Lab Windows, available
from National Instruments.
Brenner, p. 26, 11-23 (emphasis added).
[FF10]
The output of the photon counters is collected by computer
304, where it can be stored, analyzed, and viewed on video
360.
Brenner, p. 26, l. 38 to p. 27, l. 1 (emphasis added).
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[FF11]
The stability and reproducibility of the positional localization in
scanning will determine, to a large extent, the resolution for
separating closely spaced microparticles. Preferably, the
scanning systems should be capable of resolving closely spaced
microparticles, e.g. separated by a particle diameter or less.
Brenner, p. 27, ll. 4-7.
Discussion
The issue is this rejection is whether Brenner describes the
claimed system comprising a [4] “signal tracking means effective to
correlate the optical signals from each of the microparticles in each of
the sequence of digital images with said center of said microparticle.”
Limitation [4] appears in both independent claims 1 and 29 involved
in this appeal.
Brenner describes a computer loaded with software for determining
the position of microparticles and correlating these positions in successive
images (FF8 & FF11). Brenner also describes detecting optical signals from
the particles (FF8 & FF11) as recited in claim 1. However, the Examiner
did not provide sufficient evidence that Brenner teaches a computer that is
able to correlate the optical signals with the microparticle centers as required
by limitation [4] of the claims.
The Examiner states that Brenner performs a correlation with
microparticle centers, citing Brenner’s disclosure at page 26, lines 7-10 &
11-38; page 35, lines 23-39. RAN (“Right of Appeal Notice”) 6. We have
reviewed this disclosure and find evidence that Brenner registers the
positions of microparticles in an array, but none that Brenner determines the
microparticle centers.
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Life contends that Brenner’s “two-dimensional images include
positional registration information for the microparticle centers” and cites
page 35, lines 23-34 for support. Life Resp’t Br. 8. The most pertinent
passage in this disclosure is as follows:
The avidinated slide with the attached microparticles is
examined with a scanning fluorescent microscope. . . . The
excitation beam and fluorescent emissions are delivered and
collected respectively, through the same objective lens. . . . The
computer generates a two dimensional map of the slide which
registers the positions of the microparticles.
In other words, Life takes the position that because a complete scan
was accomplished of the slide on which the microparticles emitting
fluorescence optical signals were arrayed, Brenner would necessarily
measure the optical signals of the microparticle centers. This argument is
not persuasive.
The claim requires a [4] “signal tracking means . . . to correlate the
optical signals from each of the microparticles in each of the sequence of
digital images with said center of said microparticle.” We interpreted the
correlation to be accomplished separately from the recordation of the
images, the latter which is carried out by the “imaging device.” See Claim
interpretation, supra at p. 8-9. Brenner’s teaching that the entire slide is
scanned, which might include an image of the optical signals associated with
the microparticle centers, corresponds to a step accomplished by the imaging
device of claim 1. However, a complete scan does not satisfy limitation [4]
because limitation [4] requires a structure, such as a computer or other data
processing structure, which correlates the optical signals with the
microparticle centers; an image of the optical signals and microparticle
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centers is insufficient because it lacks a correlation step performed by a
computer.
For the foregoing reasons, we reverse the rejection of claims 1-4, 6,
and 14-24, 26-30, 33, and 34 under 35 U.S.C. § 102(b) as anticipated by
Brenner.

2. OBVIOUSNESS IN VIEW OF BRENNER AND SCHMIDT
Claims 7-10 and 13 stand rejected under 35 U.S.C. § 103 as obvious
over Brenner in view of Schmidt.
Claim 7 is dependent on claim 1 and further recites “the system is
configured to designate a first pixel for determining characteristics of an
optical signal generated at a microparticle, the first pixel being correlated
with the center of the microparticle.
The Examiner did not meet the burden of establishing that claim 7
would have been obvious in view of Brenner and Schmidt at the time of the
invention.
Pointing to disclosure on page 979 of Schmidt, the Examiner found
that Schmidt disclosed a system “configured to designate a first pixel for
determining characteristics of an optical signal generated at a microparticle,
the first pixel being correlated with the center of the microparticle.” RAN
11. The cited disclosure from Schmidt is as follows:
“In a few cases, the centroid of the bright portion of the DIC image
was determined from the weighted pixel intensity without using cross-
correlation analysis.” Schmidt, p. 979 (in section titled “Nanometer-
precision Analysis of Bead Position”).
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The Examiner did not provide an explanation as to how determining
the centroid of the bright portion of the DIC image from “the weighted pixel
intensity” corresponds to the limitation recited in claim 7.
Illumina provided a declaration by Dr. Jeff Gelles, who was a
Professor of Biochemistry and Molecular Pharmacology at Brandeis
University in Waltham, Massachusetts, at the time the declaration was
executed. Gelles Decl. ¶ 1. Dr. Gelles testified in his written declaration
that he used “imaging technologies in [his] research, including differential
interference contrast microscopy and multi-wavelength single molecule
fluorescence microscopy.” Gelles Decl. ¶ 5. Based on his experience and
education, we conclude that Dr. Gelles is qualified to testify in this matter.
Gelles Decl. ¶¶ 3-6. Dr. Gelles offered opinion testimony that he did “not
understand the Schmidt reference to disclose or suggest any assignment of
pixels for determining properties of optical signals (or for any other purpose)
following determination of the microparticle position.” Gelles Decl. ¶ 50.
Dr. Gelles’s testimony is consistent with the paucity of Schmidt’s disclosure
on what is meant by “weighted pixel intensity.”
Life argues:
To the extent Patent Owner relies on the Gelles
Declaration to argue that Schmidt does not contemplate ‘the
designation of specific pixels for 'determining characteristics of
an optical signal generated at a microparticle'“ (PO Response to
ACP, pp. 18-19 and Brief, pp. 11-12, citing Declaration at ¶¶
48-51), that reliance is misplaced for the same reasons detailed
above in Section (VII)(A)(1)(b).
Life Resp’t Br. 13.
Section (VII)(A)(1)(b) of Life’s Respondent Brief addresses the
sufficiency of Dr. Gelles Declaration. Life Resp’t Br. 7-8. Life contends the
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Dr. Gelles’s declaration is legally and substantively deficient, and provides
no analysis of Brenner to support his conclusion. Id. at 7.
We agree with Life that Dr. Gelles’s testimony regarding claim 7 is
largely opinion-based. However, we have relied on it only to the extent it is
consistent with Illumina’s arguments that the Examiner’s case is deficient.
With respect to the assignment of pixels to microparticles, Life
addresses Brenner, but not Schmidt. Life Resp’t Br. 8 & 13. Life did not
explain how Schmidt’s disclosure described a system “configured to
designate a first pixel for determining characteristics of an optical signal
generated at a microparticle, the first pixel being correlated with the center
of the microparticle” as recited in claim 7. Life’s arguments are therefore
defective for the same reason we found the Examiner’s argument deficient.
Accordingly, for the foregoing reasons, we reverse the rejection of
claim 7, and dependent claims 8-10 and 13.

3 & 4. OBVIOUSNESS IN VIEW OF BRENNER AND GELLES;
BRENNER AND HICKS
Claims 7-10 and 13 stand rejected under 35 U.S.C. § 103 as obvious
over Brenner in view of Gelles. Claims 7-12 stand rejected under 35 U.S.C.
§ 103 as obvious over Brenner in view of Hicks.
The Examiner found that Brenner combined with Gelles or Hicks
rendered the subject matter of claim 7, and dependent claims 8-10 and 13
obvious under 35 U.S.C. § 103. RAN 11. The Examiner found:
Gelles and Hicks also each teach determining the positions of
microparticles on a detected image (Gelles, page 450, Figure 1
and corresponding caption; Hicks, page 233, “Microscopy” and
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“Image Analysis,” and page 237, Figure 3 and corresponding
caption). Gelles and Hicks therefore each teach designating a
first pixel for at least determining position characteristics of an
optical signal generated at a microparticle, the first pixel
corresponding to (or correlated with) the center of the
microparticle.
RAN 11-12.

Gelles
Gelles described the movement of beads coated with kinesin on a
glass coverslip to which taxol-stabilized microtubules were adhered. Gelles,
p. 450, second col., ll. 4-8. Gelles recorded a video of the movement of the
beads on the glass. Gelles, p. 450, second col., second paragraph. In the
description of Figure 1, Gelles disclosed the methodology to determine the
position of the beads on the coverslip. It is true that Gelles describes using
pixels to determine the position of the beads on the glass slip, but the
Examiner did not provide evidence that such description was a disclosure of
“designat[ing] a first pixel for determining characteristics of an optical
signal generated at a microparticle, the first pixel being correlated with the
center of the microparticle” as required by claim 7. As the Examiner did not
meet the burden of establishing prima facie obviousness, we are compelled
to reverse the rejection of independent claim 7 and dependent claims 8-10
and 13.

Hicks
Hicks tracked movement of latex microspheres (FS) on fibroblasts.
Hicks, p. 231. Hicks described using pixel intensities to analyze images. Id.
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at p. 233 (“Image Analysis”). The Examiner points to this disclosure, but
fails to explain how it describes the claimed limitation to “designate a first
pixel for determining characteristics of an optical signal generated at a
microparticle, the first pixel being correlated with the center of the
microparticle” as required by claim 7.
Dr. Gelles testified that he does “not understand Hicks to disclose or
suggest a system ‘configured to designate a first pixel for determining
characteristics of an optical signal generated at a microparticle’ as recited in
claim 7 (as amended) of the '994 patent.” Gelles Decl. ¶ 80. Dr. Gelles
supported his opinion with scientific reasoning. Id. at ¶¶ 74, 75, 81, and 82.
For example, Dr. Gelles explained that Hicks describes “convolution,” “a
mathematical function that, in essence, compares a group of pixels including
and surrounding a microparticle image with a Gaussian (bell) curve. The
pixels compared include both pixels with a fluorescent signal and pixels with
a low (background) signal.” Id. at ¶ 74.
Life provides an explanation as to how Hicks is said to meet
limitations of dependent claims 11 and 12. Life Resp’t Br. 14. However,
claims 11 and 12 depend upon claim 7 and insufficient evidence has not
been provided that the limitations of claim 7 are met by Hicks.
As the Examiner did not meet the burden of establishing prima facie
obviousness, we are compelled to reverse the rejection of independent claim
7 and dependent claims 8-12.

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6. OBVIOUSNESS IN VIEW OF BRENNER AND HANSEN
Claims 5 stands rejected under 35 U.S.C. § 103 as obvious in view of
Brenner and Hansen. Claim 5 depends on claim 1, and further recites
“wherein the coefficient of variation of the diameters of said microparticles
is less than two percent.” As we reversed the rejection of claim 1, and the
Examiner did not provide evidence that Hansen described the deficiencies
we found in Brenner, we are compelled to reverse the rejection. See RAN
12; Life Technologies Resp’t Br. 15.

CROSS APPEAL
Life appeals the Examiner’s determination not to adopt the following
rejections:
1. Rejection of claims 25, 31, and 35 under 35 U.S.C. § 102 as
anticipated by Brenner.
2. Rejections of claims 29-31 and 33-35 under 35 U.S.C. § 314 as
impermissibly enlarging the scope of the claims.
3. Rejection of claims 1-4 under 35 U.S.C. § 102 as anticipated by
Lee.7
4. Rejection of claims 1, 3, and 4 under 35 U.S.C. § 102 as
anticipated by Schmidt.
5. Rejection of claims 1-4 under 35 U.S.C. § 103 as obvious over
Gelles.

7 Ann A. Lee et al. Biaxial Strain System for Cultured Cells, U.S. Patent
6,057,150 (granted May 2, 2000) (Lee).
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6. Rejection of claim 5 under 35 U.S.C. § 103 as obvious over Lee,
Gelles, and Schmidt, in view of Hansen.
7. Various rejections of claims 1-4 under 35 U.S.C. § 103. Life
Appeal Br., Ex. A.
8. Rejections of claims 1-4 under 35 U.S.C. § 103 as being obvious
over the Brenner, Lee, Schmidt, or Gelles reference in view of the NIH
Image Manual.8

1. ANTICIPATION BY BRENNER
Claims 25, 31, and 35 each have the limitation that the microparticles
are “closely packed.” Claim 25 depends on claim 1; claim 31 depends on
claim 30, which depends on independent claim 29; claim 35 depends on
claim 34, which depends on claim 33, which depends on claim 29.
Each of claims 25, 31, and 35 incorporate the limitation of a “signal
tracking means effective to correlate the optical signals from each of the
microparticles in each of the sequence of digital images with said center of
said microparticle.” We found that Brenner does not describe this limitation.
Consequently, as dependent claims 25, 31, and 35 each require this
limitation, there is sufficient evidence that they are anticipated by Brenner.
We thus affirm the Examiner’s decision not to adopt the anticipation
rejection of claims 25, 31, and 35 over Brenner.

8 NIH Image Manuel, NIH Image Version 1.58.
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2. SECTION 314 REJECTION
The Examiner did not adopt the rejection of claims 29-31 and 33-35
under 35 U.S.C. § 314 as impermissibly enlarging the scope of the ‘994
patent claims. Claim 29 comprises an optical train “configured to collect
and focus the sequence of optical signals from the microparticles.” The
original claims used the language “effective to” rather than “configured to.”
Life contends that the recitation of “configured to” expands the scope of the
‘994 patent claims because
the original claim language, “effective to,” could be interpreted
as meaning that the claimed structure actually accomplishes the
recited function, while the new language, “configured to,”
could be interpreted as meaning merely that the structure is
capable of performing the recited function.
Life Appeal Br. 15.
We are not persuaded by Life’s arguments that the claim language
“configured to” recited in claim 29 is broader than the claim language in
claim 1 of “effective to.” In both cases, the claims are directed to systems
“for detecting a sequence of optical signals from each of a plurality of
microparticles during a sequence of processing steps” that comprise an
“optical train.” The terms “effective to” and “configured to” in each case
are followed by the function that the optical train is required to perform in
the claimed system. Therefore, a person or ordinary skill in the art would
reasonably construe the terms equivalently to indicate that the optical train is
capable of performing the recited function. A system is claimed, not a
method. So it would be unreasonable to read either “effective to” or
“configured to” to further mean that the function must be actually
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accomplished. Consequently, we find Life’s arguments to have no merit and
affirm the Examiner’s determination not to adopt the rejection.

3. ANTICIPATION BY LEE
The Examiner did not adopt the rejection of claims 1-4 under 35
U.S.C. § 102 as anticipated by Lee. Illumina distinguished claim 1 from Lee
based on the preamble of claim 1. The Examiner adopted Illumina’s
interpretation. Action Closing Prosecution mailed December 15, 2010
(“ACP”) at 28. We find that the Examiner erred in interpreting the claim.
Claim 1 recites in its preamble that the claimed system is “for
detecting a sequence of optical signals from each of a plurality of
microparticles during a sequence of processing steps.” According to Life,
the “sole basis for the Examiner's withdrawal of the rejection of Lee was that
‘the microparticles in the system disclosed by Lee are not subject to
processing steps as defined by the Bridgham [‘994 patent] specification
during the observance of the microparticles’ as purportedly required by the
preamble of claim 1.” Life Appeal Br. 21. Life Technologies argues that
the preamble phrase “during a sequence of processing steps” is not limiting,
and there is no need for Lee to disclose it to anticipate. Id.
Illumina contends that the Examiner did not err in not adopting the
rejection. Illumina argues:
Thus, the phrase “sequence of processing steps” [as recited in
the claim preamble] is unambiguously descriptive of the
“sequence of optical signals” element. (See RAN, at 13). Based
on this interpretation, the Examiner correctly determined that
the claimed system does not encompass any “system for
detecting a sequence of optical signals from each of a plurality
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of microparticles,” that may be operated “during a sequence of
(generic) processing steps.” (RAN, at 13). Although the entire
phrase “detecting a sequence of optical signals from each of a
plurality of microparticles during a sequence of processing
steps” does not appear in the body of claim 1, the elements of
“the sequence of optical signals from the microparticles,” “said
signals,” and “the optical signals from each of the
microparticles” each refer to the optical signals that are
generated during, and as a result of, the “sequence of processing
steps.”
Illumina Resp’t Br. 7.

Legal Principles
“Preamble language that merely states the purpose or intended use of
an invention is generally not treated as limiting the scope of the claim.”
Bicon, Inc. v. Straumann Co., 441 F.3d 945, 951 (Fed. Cir. 2006).
If the body of the claim ‘sets out the complete invention,’
the preamble is not ordinarily treated as limiting the scope of
the claim. Schumer v. Lab. Computer Sys., Inc., 308 F.3d 1304,
1310 (Fed. Cir. 2002)). However, the preamble is regarded as
limiting if it recites essential structure that is important to the
invention or necessary to give meaning to the claim. [citations
omitted]. . . When limitations in the body of the claim rely upon
and derive antecedent basis from the preamble, then the
preamble may act as a necessary component of the claimed
invention.” Eaton Corp. v. Rockwell Int'l Corp., 323 F.3d
1332, 1339 (Fed. Cir. 2003).
Id. at 952.

Issue
The issues in this rejection are thus: is the invention set forth in the
body of the claim is complete or does the claimed invention require the
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preamble limitation “during a sequence of processing steps” for
completeness; and is the preamble limitation is merely a “purpose or
intended use” of the claimed invention?

Discussion
The claimed “optical train,” “imaging device,” and “signal tracking
means” each have recited functions. These components are not simply
general purpose structures, but must be “effective” or have the ability to
carry out the recited function. See Claim interpretation, supra at p. 9. With
respect to the “optical train,” the claim requires it to be able “to collect and
focus the sequence of optical signals from the microparticles, and to record
at least one optical characteristic of each microparticle.” The “imaging
device” must be able to “generate and record a sequence of digital images of
the microparticles” comprising the optical signals. The “signal tracking
means must “correlate the optical signals from each of the microparticles in
each of the sequence of digital images with said center of said
microparticle.” These functions are express limitations that constrain the
“optical train,” “imaging device,” and “signal tracking means” to structures
which are able to perform the recited functions. The components must
therefore be capable of capturing sequences of signals and sequences of
digital images.
The claim preamble that the signals and images are captured “during a
sequence of processing steps” does not further limit or define the
subsequently recited structures “optical train,” “imaging device,” and “signal
tracking means,” but rather simply reflects the intention that the system is
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used during such processing steps. The processing steps constitute an
environment in which the system is capable of being used, and is intended to
be used, but it does not change the structure or capability of the subsequently
recited components. In fact, there is no component recited in the body of the
claim which would perform the sequence of processing steps. Thus, we do
not see, and Illumina has not adequately explained, how the claimed
preamble is a necessary component of the claimed invention and necessary
to complete the invention recited in the claim body.
In contrast, claim 29 which has similar language adds the additional
limitation of “a fluidics controller effective to deliver reagents to the flow
cell for a sequence of processing steps.” Absent express language in the
claim, we will not read this imitation into claim 1. Life Appeal Br. 19-20.
For the foregoing reasons, we conclude that the Examiner erred in not
adopting the rejection of claims 1-4 as anticipated by Lee.

4. ANTICIPATION BY SCHMIDT
Life proposed a rejection of claims 1, 3, and 4 under 35 U.S.C. § 102
as anticipated by the Schmidt reference which the Examiner initially
adopted, but subsequently withdrew. ACP 31-32.
Schmidt described the movement of colloidal gold particles on cells.
Schmidt, p. 977. The gold particles were coated with anti-B1 integrin
antibody. Id. The antibody bound to integrin on the cells, attaching the
colloidal gold particles to the cell surface. Id. “Small gold aggregates
[attached to the antibody] were rapidly transported preferentially to the
leading edge of the lamellipod where they resumed diffusion restricted along
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the edge.” Id. The transport of the colloidal gold particles on the cells was
tracked using video microscopy. Id. The Examiner found that “Schmidt
does not disclose a planar array of uniformly sized spherical microparticles”
as recited in independent claim 1. ACP 31-32.
Life contends that “Schmidt does disclose such a planar array in that
Schmidt detects and monitors the displacements of microparticles in an array
on a substantially planar surface of cultured adherent cells on a glass slide,
where microbeads are placed into contact with the cells. Indeed, Schmidt
discloses two planar arrays, one comprising cells on the glass slide and one
comprising microbeads, smaller in scale than the cells.” Life Appeal Br. 22.
These arguments are not persuasive. First, Life has not provided
persuasive evidence that cells are microparticles as that term would be
interpreted in light of the ‘994 patent specification. Secondly, Life has not
explained how colloidal particles distributed on the three-dimensional
surface of cells constitutes a planar array as that term would be construed in
light of the patent. Consequently, we agree with Illumina that the Examiner
did not err in not adopting the rejection of claims 1, 3, and 4 as anticipated
by Schmidt.

5. OBVIOUSNESS IN VIEW OF GELLES
Life proposed a rejection of claims 1-4 under 35 U.S.C. § 103 as
obvious over Gelles which the Examiner initially adopted, but subsequently
withdrew. ACP 36-37.
Gelles describes a system for recording, analyzing, and determining
precise positional information of microscopic plastic beads (i.e.,
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microparticles) on a glass coverslip (i.e., a planar array) as the
microparticles, driven by kinesin, attach to and move along microtubules in
vitro (i.e., a sequence of processing steps). Gelles, p. 450, abstract and
column 2, first paragraph, through page 451, first partial paragraph; and Fig.
2).
Life contends that the Examiner did not adopt the rejection because
Gelles did not subject the microparticles to processing steps and because
Gelles did not disclose uniform particles, both of which the Examiner stated
are required by independent claim 1. Life Appeal Br. 23; see ACP 36-37.
Illumina contends that Gelles does not disclose a sequence of processing
steps. Illumina Resp’t Br. 10.
As discussed above, the preamble phrase “during a sequence of
processing steps” is not limiting, and there is no need for Gelles to disclose it
to anticipate or render the claim obvious. Because the Examiner erred in
interpreting the claim and Illumina has not otherwise distinguished the claim
over Gelles, we find that the Examiner erred in withdrawing the rejection of
claims 1-4 as obvious in view of Gelles.

6. OBVIOUSNESS REJECTIONS OVER LEE, SCHMIDT, AND
GELLES IN VIEW OF HANSEN
Life proposed a rejection of claim 5 under 35 U.S.C. § 103 as obvious
over Lee, Gelles, and Schmidt, in view of Hansen. Life contends the
Examiner
declined to adopt obviousness rejections based on Lee, Schmidt
or Gelles, in view of Hansen solely because the Examiner found
that Lee, Schmidt, and Gelles each purportedly fail to anticipate
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and/or render independent claim 1 obvious. See ACP, pp. 20-
21, 31, 35-36, and 41. As demonstrated above, the Examiner
should not have withdrawn the rejections of claim 1 in view of
Lee, Schmidt, and Gelles. Because claim 1 is anticipated by
and/or obvious over each of Lee, Schmidt, and Gelles, the
Examiner also erred in failing to adopt the above-identified
rejections of claim 5.
Life Appeal Br. 24.
We concluded that the Examiner erred in not adopting the rejections
of the claims as anticipated by the Lee and Gelles publications. However,
we concluded that the Examiner properly determined that the claims were
not anticipated by Schmidt. Illumina did not dispute that Hansen in view of
Lee and Gelles described or suggested the subject matter of claim 5.
Illumina Resp’t Br. 10. Therefore, we shall reverse the Examiner’s
determination not to adopt the obviousness rejection of claim 5 over Lee and
Gelles in view of Hansen, but affirm as it pertains to Schmidt.

7. VARIOUS NON-ADOPTED OBVIOUSNESS REJECTIONS
Life proposed numerous rejections of claims 1-4 under 35 U.S.C. §
103 that Life contends the Examiner did not consider because it “it would be
‘improper’ to enter a multiple reference obviousness rejection where a single
reference obviousness rejection over the same reference had already been
applied.” Life Appeal Br. 26. Life contends that the “Examiner's refusal to
adopt those obviousness SNQs solely because an anticipation or obviousness
rejection over the same reference had already been applied is not legally
tenable, is contrary to the MPEP, and is in tension with the prohibition
against piecemeal prosecution.” Id.
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In the Request for Reexamination, Life proposed numerous rejections
under 35 U.S.C. § 103. For example Gelles was combined with each of the
following: Brenner, Lee, Schmidt, Douglass, Stern, King, Luck, Sizto,
DiMilla, Dow, Wernet, Wilson, Brandriss, NIH Image Manual, Brenner &
Brandriss, Lee & Brandriss, Schmidt & Brandriss, or Douglas & Brandriss,
in eighteen separate rejections. The Examiner indicated that the rejections
raised a substantial new question of patentability. Decision Granting Inter
Partes Reexamination, May 10, 2010, p. 4-6. However, in a subsequent
Office Action, the Examiner did not adopt all of them because the Examiner
found that Gelles already described the limitations for which the additionally
secondary references were cited. Non-Final Office Action, May 10, 2010, p.
13.
We agree with the Examiner. Relying on 18 separate rejections for
the same limitations, and for the same limitations already identified in the
primary reference, is cumulative and unnecessarily duplicative. The
limitations were addressed by the Examiner in adopted rejections, making
the non-adopted rejections moot.
Moreover, had Life believed that the adopted rejections were
inadequate, Life could have pointed out the differences in the proposed
rejections to the Examiner, and explained why they were necessary to
establish unpatentability. Under 35 U.S.C. § 314(c), inter partes
reexaminations are to be conducted with “special dispatch.” Cumulative
rejections add to the time it takes to conduct an appeal, and thus limiting the
issues is important to comply with 35 U.S.C. § 314(c).

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8. OBVIOUSNESS IN VIEW OF NIH IMAGE MANUAL
The Examiner declined to consider Requester’s proposed rejections
based on the NIH Image Manual because Life did not establish that it
qualified as prior art against the '994 patent. ACP 42-43; RAN 15. Life
Challenges this determination. Life contends:
Requester has established, at least prima facie, that the manual
was available at the same time as the software. As explained in
the previously-submitted 1995 Rasband Reference (see
Requester's August 9, 2010 submission, p. 24), NIH Image
software is accompanied by a user manual. Thus, given that the
1995 Rasband Reference explains that NIH Image software is
accompanied by a user manual, the NIH Image software
referenced in the 1995 Opalenik Reference would have
included the associated user manual. In the absence of any
evidence to the contrary, and in light of the evidentiary standard
for demonstrating that a reference is prior art, Requester has
adequately established that the NIH Image Manual v. 1.58 is
prior art.
Life Appeal Br. 28.

Legal Principles
“Because there are many ways in which a reference may be
disseminated to the interested public, ‘public accessibility’ has
been called the touchstone in determining whether a reference
constitutes a ‘printed publication’ bar under 35 U.S.C.
§102(b).” In re Hall, 781 F.2d 897, 898-99 (Fed. Cir. 1986)
(emphasis added). “A given reference is ‘publicly accessible’
upon a satisfactory showing that such document has been
disseminated or otherwise made available to the extent that
persons interested and ordinarily skilled in the subject matter or
art exercising reasonable diligence, can locate it.” Bruckelmyer
v. Ground Heaters, Inc., 445 F.3d 1374, 1378 (Fed. Cir. 2006).
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SRI International Inc. v. Internet Security Systems Inc., 511 F.3d 1186, 1194
(Fed. Cir. 2008).

Discussion
The Examiner did not accept Life’s arguments that the NIH Image
Manual was prior art because the Manual did not have publication date
(Non-Final Office Action, dated May 10, 2010, p. 12). Life responded by
providing a publication by Rasband and Bright (Microbeam Analysis, 4:137-
149 (1995)) which disclosed: “NIH Image comes with many other files: a
user manual ‘About NIH Image [.]’” Rasband, p.137, second col, first full
paragraph. However, Life did not establish the document submitted by them
titled “NIH Image (Version 1.58)” is the same manual referred to by
Rasband and Bright. The evidence provided by Life is insufficient to
establish that NIH Image (Version 1.58) was publically accessible prior to
the effective filing date of the ‘994 Patent.

SUMMARY
Appeal
1. The rejection of claims 1-4, 6, 14-24, 26-30, 33, and 34 as
anticipated by Brenner is reversed.
2. The rejection of claims 7-10 and 13 as obvious over Brenner in
view of Schmidt is reversed.
3. The rejection of claims 7-10 and 13 as obvious over Brenner in
view of Gelles is reversed.
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4. The rejection of claims 7-12 as obvious over Brenner in view of
Hicks is reversed.
5. The rejection of claim 5 as obvious over Brenner in view of
Hansen is reversed.

Cross-Appeal
1. The Examiner’s determination not to adopt the rejection of claims
25, 31, and 35 under 35 U.S.C. § 102 as anticipated by Brenner is affirmed.
2. The Examiner’s determination not to adopt the rejection of claims
29-31 and 33-35 under 35 U.S.C. § 314 as impermissibly enlarging the
scope of the claims is affirmed.
3. The Examiner’s determination not to adopt the rejection of claims
1-4 under 35 U.S.C. § 102 as anticipated by Lee is reversed.
4. The Examiner’s determination not to adopt the rejection of claims
1, 3, and 4 under 35 U.S.C. § 102 as anticipated by Schmidt is affirmed.
5. The Examiner’s determination not to adopt the rejection of claims
1-4 under 35 U.S.C. § 103 as obvious over Gelles is reversed.
6. The Examiner’s determination not to adopt the rejection of claim 5
under 35 U.S.C. § 103 as obvious over Lee and Gelles in view of Hansen is
reversed.
7. The Examiner’s determination not to adopt the rejection of claim 5
under 35 U.S.C. § 103 as obvious over Lee, Gelles, and Schmidt in view of
Hansen is reversed.
8. The Examiner’s determination not to adopt various obviousness
rejections under 35 U.S.C. § 103 is affirmed.
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9. The Examiner’s determination not to adopt the rejection of claims
1-4 under 35 U.S.C. § 103 as obvious over the Brenner, Lee, Schmidt, or
Gelles reference in view of the NIH Image Manual is affirmed.

NEW GROUNDS OF REJECTION
37 C.F.R. § 41.77(a) states that “[t]he reversal of the examiner’s
determination not to make a rejection proposed by the third party requester
constitutes a decision adverse to the patentability of the claims which are
subject to that proposed rejection which will be set forth in the decision of
the Board of Patent Appeals and Interferences as a new ground of rejection.”
Accordingly, for the reasons given above, we enter the following new
grounds of rejection:

Claims 1-4 are rejected under 35 U.S.C. § 102 as anticipated by Lee.
Claims 1-4 are rejected under 35 U.S.C. § 103 as obvious over Gelles.
Claim 5 is rejected under 35 U.S.C. § 103 as obvious over Lee and
Gelles in view of Hansen.
Claim 5 is rejected under 35 U.S.C. § 103 as obvious over Lee,
Gelles, and Schmidt in view of Hansen

This decision contains new grounds of rejection pursuant to 37 C.F.R.
§ 41.77(b) which provides that “[a]ny decision which includes a new ground
of rejection pursuant to this paragraph shall not be considered final for
judicial review.” Accordingly, no portion of the decision is final for
purposes of judicial review. A requester may also request rehearing under
37 C.F.R. § 41.79, if appropriate, however, the Board may elect to defer
issuing any decision on such request for rehearing until such time that a final
decision on appeal has been issued by the Board.
For further guidance on new grounds of rejection, see 37 C.F.R.
§ 41.77(b)-(g). The decision may become final after it has returned to the
Board. 37 C.F.R. § 41.77(f).
37 C.F.R. § 41.77(b) also provides that the Patent Owner, WITHIN
ONE MONTH FROM THE DATE OF THE DECISION, must exercise one
of the following two options with respect to the new grounds of rejection to
avoid termination of the appeal as to the rejected claims:
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(1) Reopen prosecution. The owner may file a response requesting
reopening of prosecution before the examiner. Such a response must be
either an amendment of the claims so rejected or new evidence relating to
the claims so rejected, or both.
(2) Request rehearing. The owner may request that the proceeding be
reheard under § 41.79 by the Board upon the same record. …
Any request to reopen prosecution before the examiner under 37
C.F.R. § 41.77(b)(1) shall be limited in scope to the “claims so rejected.”
Accordingly, a request to reopen prosecution is limited to issues raised by
the new ground(s) of rejection entered by the Board. A request to reopen
prosecution that includes issues other than those raised by the new ground(s)
is unlikely to be granted. Furthermore, should the patent owner seek to
substitute claims, there is a presumption that only one substitute claim would
be needed to replace a cancelled claim.
A requester may file comments in reply to a patent owner response.
37 C.F.R. § 41.77(c). Requester comments under 37 C.F.R. § 41.77(c) shall
be limited in scope to the issues raised by the Board's opinion reflecting its
decision to reject the claims and the patent owner's response under
paragraph 37 C.F.R. § 41.77(b)(1). A newly proposed rejection is not
permitted as a matter of right. A newly proposed rejection may be
appropriate if it is presented to address an amendment and/or new evidence
properly submitted by the patent owner, and is presented with a brief
explanation as to why the newly proposed rejection is now necessary and
why it could not have been presented earlier.
Compliance with the page limits pursuant to 37 C.F.R. § 1.943(b), for
all patent owner responses and requester comments, is required.
The examiner, after the Board’s entry of a patent owner response and
requester comments, will issue a determination under 37 C.F.R. § 41.77(d)
as to whether the Board’s rejection is maintained or has been overcome.
The proceeding will then be returned to the Board together with any
comments and reply submitted by the owner and/or requester under
37 C.F.R. § 41.77(e) for reconsideration and issuance of a new decision by
the Board as provided by 37 C.F.R. § 41.77(f).
Requests for extensions of time in this inter partes reexamination
proceeding are governed by 37 C.F.R. § 1.956. See also 37 C.F.R. § 41.79.

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REVERSED; NEW GROUNDS UNDER § 41.77(b)

Patent Owner:
REINHART BOERNER VAN DEUREN S.C.
ATTN: LINDA KASULKE, DOCKET COORDINATOR
1000 North Water Street, Suite 2100
Milwaukee, WI 53202

Third Party Requester:
ALAN HAMMOND
LIFE TECHNOLOGIES CORPORATION
ATTN: IP DEPARTMENT
5791 Van Alley Way
Carlsbad, CA 92008