III.E CAPABILITIES III.E.1 Technical Area 1: Continuous Sensing in Complex Fluid (3/241)

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SRI Proposal ERU 11
-
044 (Volume I)

31 March 2011

56

USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.E

CAPABILITIES

III.E.1

Technical Area 1: Continuous Sensing in Complex Fluid
(
3/24

1)

SRI’s headquarters is located on the San Francisco peninsula in the heart of Silicon Valley and includes
40 buildings encompassing more than 1.3 million gross square feet, located on a single 63
-
acre site in
the city of Menlo Park. SRI maintains fully equi
pped and operating laboratories in physics, life sciences,
chemistry, materials, electronics, information sciences, atmospheric sciences, and electromagnetism.

Facilities

Genalyte Ring Resonator Dev
elopment Facility (San Diego, California
)

is an optical

la
boratory
equipped with all the necessary optical assembly tools, design software, optical testing equipment
,

and
light machining capability for development of the free spac
e and fiber optic subsystems.
The optics
laboratory conducts design, construction
,

a
nd testing of all equipment for the Genalyte sensing
instrument platform.

In addition to the optical facilities described

above, Genalyte has a 1,440
ft
2

assay laboratory fully
equipped for standard Class II wet lab operati
ons, including chemical hoods.

Th
e laboratory also
supports chemical handling, microscopy, cell culture, nucleic acid amplification and
Biosafety Level 2
(
BSL
-
2)
standard practice:
In this portion of the laboratory
,

assay research and test product development
are conducted.

Genalyte is he
adquartered in the biotech corridor of Torrey Mesa La Jolla, C
alifornia,

in a leased
2,500

ft
2

facility that accommodates the science, engineering
,

and commerc
ial elements of the company.
Genalyte operates under stand
ard operating procedures
to maintain a
quality system and design control
process consistent with its level of FDA regulation.

SRI Sensor Systems Laboratory
.

SRI work in Technical Area 1 will be conducted within BSL
-
2
laboratory facilities in the Sensor Systems Laboratory (SSL) of SRI’s Physical

Sciences Division.
The
SSL

has 4,400 ft
2

of optical and biosensor laboratory space dedicated to the development and proto
-
typing of advanced biosensors and electro
-
optical systems. The labs are designed for proof
-
of
-
principle
experiments, as well as
component, subsystem, and system test and evaluation. A full complement of
bioanalytical instrumentation, optical equipment, modeling tools, and electronic test equipment is
available. SSL’s microfluidics laboratory has ultraviolet and CO
2

laser cutting to
ols, four laminators,
Argon plasma for surface treatment, a semiconductor mask tool for aligning laminate layers, measuring
and inspection microscopes, and high
-
efficiency particulate air hoods for assembly. Additionally
,

SRI
has a DNA microarray synthesis

instrument capable of synthesizing on

microscope slides, 4
"

wafers,
and 6
"

wafers
.

During Phase
I

of the proposed study, SRI will purchase a complete ring resonator
analysis system from Genalyte for evaluation, development of a customized microfluidic hou
sing, and
parallel assay development.


SSL Microfluidics Devices Laboratory


SSL Biosensors Laboratory

SRI Proposal ERU 11
-
044 (Volume I)

31 March 2011

57

USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.E.3

Technical Area 3: Intrinsic Separation from Complex Fluid
(
3/
2
4

1)

SRI Animal Facilities for Pharmacology, Pharmacokinetic, and Toxicology
Evaluations

(~ 75,000
ft
2
):

AAALAC accredited, with three separate buildings containing ~80 animal rooms and 146 large
animal runs to support rodents, rabbits, dogs,
pigs,
and nonhuman primates (NHP). Two cage washers, a
rack washer,
2

autoclaves;
3

approved NHP quarantine rooms;
4

BSL
-
2

rooms; rooms for feed mixing and
diet preparation, animal treatment, surgery, necropsy, and storage; rooms for studies using radio
labeled
materials; metabolism cages for all species; locker room with shower; emergen
cy backup power for all
3

buildings.

SRI Immunology Facilities
(~3,600 ft
2
):

Laminar flow cabinets certified for
BSL
-
2; CO
2

incubators; protein gel and immunoblot instrumentation; Tomtec automatic cell harvester; Betaplate liquid
scintillation counter; bet
a counter; gamma counter; sealed
-
source cesium irradiator;
2

inverted phase
contrast microscopes;
2

light microscopes;
6 bench
top centrifuges;
2

automated plate washers;
3

immu
-
noassay plate readers; enzyme
-
linked immunoassay spot (ELIspot) reader; Tecan I
nstruments Genesis
Robotic Sample Processor, MSD Sector Imager; BD FACSCalibur 2
-
Laser/6
-
parameter flow cytometer;
BD LSRII 3 Laser/10 parameter flow cytometer.

SRI Molecular Biology Facilities

(~2,500 ft
2
):

Eleven
connected, controlled access suites, with

associated support facilities of a w
alk
-
in cold room, autoclaves,
darkroom, media preparation station, glass washing station, and refrigerators, freezers, and ultra
-
low
freezers connected to backup power with 24

hr temperature recording and monitoring; re
al
-
time
quantitative PCR, DNA/RNA/protein manipulations and analysis, gene expression analysis, genotyping,
cell culture activities, and subcloning; real
-
time quantitative PCR (Roche LightCycler 480) in a 96 and
384 well format, Nanodrop small volume spect
rophotometer, Agilent’s capillary electrophoresis
Bioanalyzer, FluorChem SP imaging station, PCR machines, microplate reader, centrifuges, refrigerated
centrifuges, shakers, incubators, fully equipped cell culture suite, biological and chemical safety hood
s,
electrophoresis equipment, electroporator, analytical balance, pH meter, water baths, and heating blocks.

SRI Microbiology/Virology Facilities

(~2,000 ft
2
):

Four laboratories located near each other totaling
approximately 1,200 ft
2

for cell biology and
microbiology testing and research.

We have both BSL
-
2 and
BSL
-
3 laboratories. The BSL
-
3 microbiology laboratories are equipped with laminar flow ho
ods
(biosafety cabinets), bench
top high
-
speed refrigerated centrifuge, CO
2

incubator, standard incubators,
re
frigerator, freezer, light microscopes, small autoclave, water bath, and other small microbiology related
equipment.

The BSL
-
3 laboratories are approved by CDC for work with select agents.

SRI Flow
Cytometry Facility:

Facility has a dual laser
-
equipped BD
FACScalibur equipped with a 488

nm and 635
nm lasers capable of detecting multiple dyes, including FITC (525 nm), PE (575 nm), PerCP (678 nm) or
PerCP
-
Cy5.5 (695 nm) and APC (660 nm).

This flow cytometer has capability for high content screening
assays. SR
I has ordered a more powerful cytometer to enable simultaneous acquisition on 6

to
8 colors via
excitation by
3

lasers, to permit expansion of high content screening to provide more information on the
biological status of host cells and parasites using the

same number of cells, parasites, and test materials per
assay.

SRI Microanalysis

(~1200 ft
2
):

Two laboratories for working with live single cells and nanopar
-
ticles including a custom robotic system capable of dispensing droplets with both spotting and pi
ezo tips
;
custom optical microfluidic droplet analysis system for working with droplets in the picoliter to nanoliter
range including mixing, fluorescence imaging, real
-
time PCR and RT
-
PCR in
10 min

or less; facilities for
preparing metal nanoparticles wit
h control over size and conjugation to proteins; World Precision
Instruments liquid waveguide capillary cell system with peristaltic pump; Zeiss and Nikon fluorescence
microscopes and associated imaging systems; kilohertz frequency domain imaging system wi
th Vision
Research Phantom v7.3 high speed camera and FPGA processing hardware.

Revzin Group, UC Davis

(1250 ft
2
)

is h
oused in a 1250

ft
2

laboratory in the same building with
a
genomics/proteomics center,
immunology
,

and pharmacology depa
rtments. The lab
contains a 150 ft
2

cleanroom set
up for photo
-
lithography and soft lithography experiments, surface characterization equipment, potentiostats/

im
ped
ance
meters, fluorescence microscope, and tissue culture facilities.

Equipment:
We will purchase a label
-
free

rea
l
-
time analysis system for screening of various affinity
reagents (estimate $135,000). Using this system is a more cost effective method than using existing
assays that are more labor intensive.

SRI Proposal ERU 11
-
044 (Volume I)

31 March 2011

58

USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.E.4

Technical Area 4: Predictive Modeling
(
3/24

1)

C
omputational Resources of the SRI Computer Science Laboratory:

This task will be carried out
using computational facilities of SRI’s Computer Science Laboratory (CSL). CSL supports its own
research facility consisting of over 100 workstations, and over 30
file servers and CPU servers including
several high
-
end multiprocessor/multicore machines. All staff members have workstations in their
offices and are provided with high
-
end laptops as required. Most of the computing facility is running
Linux, with dedica
ted machines running FreeBSD, Mac OS X, SunOS, Solaris, AIX
,

and Digital UNIX.
Many programming languages and software tools are available via a shared file system, as well as SQL
database servers and a multi
-
seat license for MatLab. Several personal compu
ters are available running
Windows and Mac OS X. A printing service is maintained providing high
-
quality monochrome and
color printing. All of the servers, workstations and printers are connected to a high
-
capacity Cisco
switch providing 200

MB links to of
fices, and by multiple redundant links to the Internet. CSL servers
are protected by Cisco PIX. Network policy is set at default deny so that all unwanted connections to
SRI’s internal network are blocked. Telecommuting access is also supported, by means o
f dedicated
high
-
speed ISDN and DSL links to staff homes. Regular system backups are taken, and electronic media
are stored both in secure on
-
site facilities and commercial off
-
site data storage facilities.

Animal Facilities for Pharmacology, Pharmacokinet
ic
, and Toxicology Evaluations
(~75,000 ft
2
):

AAALAC accredited, with three separate buildings containing ~80 animal rooms and 146 large animal
runs to support rodents, rabbits, dogs, pigs, and
NHPs
. Two cage washers, a rack washer, two
autoclaves; three a
pproved NHP quarantine rooms; four
BSL
-
2

rooms; rooms for feed mixing and diet
preparation, animal treatment, surgery, necropsy, and storage; rooms for studies using radiolabeled
materials; metabolism cages for all species; locker room with shower; emergency backup power for all
three buildings.

Immunology Facilities

(~3,600 ft
2
): Laminar flow cabinets certified for Biosafety Level 2; CO
2

incubators; protein gel and immunoblot instrumentation; Tomtec automatic cell harvester; Betaplate
liquid scintillation counter; beta counter; gamma counter; se
aled
-
source cesium irradiator; two inverted
phase contrast microscopes; two light microscopes; six bench
-
top centrifuges; two automated plate
washers; three immunoassay plate readers; enzyme
-
linked immunoassay spot (ELIspot) reader; Tecan
Instruments Genes
is Robotic Sample Processor, MSD Sector Imager; BD FACSCalibur 2
-
Laser/6
-
parameter flow cytometer; BD LSRII 3 Laser/10 parameter flow cytometer.

Data Resources:

In addition to computational, immunology, and animal facilities, the other important
resource i
n Task 4 is data. Substantial data will be generated by DLT animal studies. For human data,
we plan to acquire clinical data sets from the SepNet consortium (see Letter of Intent from Konrad
Reinhart). We are also applying for access to the Trauma
-
Bur
n dat
abase generated by the NIH
-
funded
GlueGrant project (www.gluegrant.org)

an SRI IRB ex
emption or approval is needed.

SRI Proposal ERU 11
-
044 (Volume I)

31 March 2011

59

USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.E.5

Technical Area 5: System Integration
(
3/24

1)

Animal Facilities for Pharmacology, Pharmacokinetic, and Toxicology Evaluations

(~75,
000 ft
2
):

AAALAC accredited, with three separate buildings containing ~80 animal rooms and 146 large animal
runs to support rodents, rabbits, dogs, pigs, and
nonhuman

primates (NHP). Two cage washers, a rack
washer, two autoclaves; three approved NHP quara
ntine rooms; four Biosafety Level 2 (BSL
-
2) rooms;
rooms for feed mixing and diet preparation, animal treatment, surgery, necropsy, and storage; rooms for
studies using radiolabeled materials; metabolism cages for all species; locker room with shower; emer
-
gency backup power for all three buildings.

Immunology Facilities

(~3,600 ft
2
):
Laminar flow cabinets
certified for
BSL
-
2; CO
2

incubators; protein gel and immunoblot instrumentation; Tomtec automatic cell
harvester; Betaplate liquid scintillation counter; beta counter; gamma
counter
; sealed
-
source cesium
irradiator; two inverted phase contrast microscopes; two light microscopes;
six bench
-
top centrifuges;
two automated plate washers; three immunoassay plate readers; enzyme
-
linked immunoassay spot
(ELIspot) reader; Tecan Instruments Genesis Robotic Sample Processor, MSD Sector Imager; BD
FACSCalibur 2
-
Laser/6
-
parameter flow cytomet
er; BD LSRII 3 Laser/10 parameter flow cytometer.

Microbiology/Virology Facilities

(~2,000 ft
2
):

Four laboratories located near each other totaling
approximately 1,200 ft
2

for cell biology and microbiology testing and research.

We have both BSL
-
2
and BSL
-
3

laboratories. The BSL
-
3
microbiology

laboratories are equipped with laminar flow hoods
(biosafety cabinets), bench
-
top high
-
speed refrigerated centrifuge, CO
2

incubator, standard incubators,
refrigerator, freezer, light microscopes, small autoclave, water

bath, and other small microbiology
related equipment.

The BSL
-
3 laboratories are approved by CDC for work with select agents.

Example of System Integration Project of Similar Scope and Complexity

Develop
ment

of
C
omplex
Apheresis M
achine for
LDL extraction

from blood.

The machine included a process to
separate red blood cells from plasma and a process to treat plasma with a dialysate using custom hollow
-
fiber filters. Work included development of the process, breadboard development, product engineering,
pro
duct design, user interface development, testing and validation. Design processes followed FDA
guidelines for medical device development and included regulatory experts on the team. Some of the
innovations included a novel continuous
-
flow miniature centrif
uge, new sensors to detect solvent levels
in plasma and a novel integrated cassette for the disposable. The project scope was $12M and included a
technical team of more than 20 individuals from different disciplines and organizations. The device was
design
ed to capture and retain circulating antibodies and return the antibody
-
free plasma to the subject.
The device required a very small extracorporeal volume (25 mL) due to the small blood volume of
rabbits (200 mL). So the emphasis was on minimizing fluid ho
ldup in the device and verifying that the
proposed capture column did not unacceptably alter the blood or plasma being returned. The system is
being used at SRI to collect antibodies from transgenic rabbits and was developed to support an NIH
effort to cre
ate a vaccine for
Botulinum neurotoxin
. Work involved concept development through final
product, including development of the disposable fluid circuit, component selection and integration,
controller, and user interface design. The machine is being used su
ccessfully at SRI.

(
a
)


(b)


(c)


Development of
an a
pheresis
d
evice for
r
abbits
: (a) Breadboard apheresis machine; (b)

Final
design; (c) Rabbit apheresis machine
.

SRI Proposal ERU 11
-
044 (Volume I)

31 March 2011

60

USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.E.6

Technical Area 6: System Validation
(
3/24

1)

Animal Facilities for Pharmacology, Pharmacokinetic, and Toxicology Evaluations
(~ 75,000 ft
2
):

AAALAC accredited, with three separate buildings containing ~80 animal rooms and 146 large animal
runs to support rodents, rabbits, dogs,
pigs,
and
NHPs
. Two ca
ge washers, a rack washer, two
autoclaves; three approved NHP quarantine rooms; four Biosafety Level 2 (BSL
-
2) rooms; rooms for
feed mixing and diet preparation, animal treatment, surgery, necropsy, and storage; rooms for studies
using radiolabeled materia
ls; metabolism cages for all species; locker room with shower; emergency
backup power for all three buildings.

Immunology Facilities
(~3,600 ft
2
):

Laminar flow cabinets certified for
BSL
-
2; CO
2

incubators; protein
gel and immunoblot instrumentation; Tomtec automatic cell harvester; Betaplate liquid scintillation
counter; beta counter; gamma counter; sealed
-
source cesium irradiator; two inverted phase contrast
microscopes; two light microscopes;
six bench
-
top centrifuges; two automated plate washers; three
immunoassay plate readers; enzyme
-
linked immunoassay spot (ELIspot) reader; Tecan Instruments
Genesis Robotic Sample Processor, MSD Sector Imager; BD FACSCalibur 2
-
Laser/6
-
parameter flow
cytomet
er; BD LSRII 3 Laser/10 parameter flow cytometer.

Molecular Biology Facilities
(~2,500 ft
2
):

Eleven connected, controlled access suites, with associated
support facilities of a walk
-
in cold room, autoclaves, a darkroom, media preparation station, glass
was
hing station, and refrigerators, freezers, and ultra
-
low freezers connected to backup power with 24 hr
temperature recording and monitoring; all suites with labware and laboratory instrumentation for
molecular biology research, including real
-
time quantita
tive PCR, DNA/RNA/protein manipulations and
analysis, gene expression analysis, genotyping, cell culture activities, and subcloning; specific equip
-
ment: real
-
time quantitative PCR (Roche LightCycler 480) in a 96 and 384 well format, Nanodrop small
volume
spectrophotometer, Agilent’s capillary electrophoresis Bioanalyzer, FluorChem SP imaging
station, PCR machines, microplate reader, centrifuges, refrigerated centrifuges, shakers, incubators, fully
equipped cell culture suite, biological and chemical safety

hoods, electrophoresis equipment, electro
-
porator, analytical balance, pH meter, water baths, and heating blocks.

Microbiology/Virology Facilities
(~2,000 ft
2
):

Four laboratories located near each other totaling
approximately 1,200 ft2 for cell biology an
d microbiology testing and research.

We have both BSL
-
2
and BSL
-
3 laboratories. The BSL
-
3 microbiology laboratories are equipped with laminar flow hoods
(biosafety cabinets), bench
-
top high
-
speed refrigerated centrifuge, CO2 incubator, standard incubators,

refrigerator, freezer, light microscopes, small autoclave, water bath, and other small microbiology
related equipment.

The BSL
-
3 laboratories are approved by CDC for work with select agents.

Flow Cytometry Facility
:

Facility has a dual laser
-
equipped BD F
ACScalibur equipped with a 488 nm
and 635 nm lasers capable of detecting multiple dyes, including FITC (525 nm), PE (575 nm), PerCP
(678 nm) or PerCP
-
Cy5.5 (695 nm) and APC (660 nm).

This flow cytometer has capability for high
content screening assays. SRI

has ordered a more powerful cytometer to enable simultaneous acquisition
on 6

8 colors via excitation by three lasers, to permit expansion of high content screening to provide
more information on the biological status of host cells and parasites using the

same number of cells,
parasites, and test materials per assay.

Robotics Group: Hardware Fabrication and Test Facilities
(~2,400 ft
2
):

Five laboratories dedicated
to design and development of hardware systems including FMBC platforms. The labs are equipped

with
oscilloscopes, power supplies, function generators, stereo microscopes, a high
-
speed camera, optical
displacement sensor, a magnetizer, load (force) cells, large sheet cutter/plotter, and a fused deposition
modeling 3
-
D printer.

CAD/CAM capabilities
include PC
-
based Solidworks for mechanical design and
COMSOL

for finite element analysis.

SRI Proposal ERU 11
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044 (Volume I)

31 March 2011

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USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.F

COSTS, SCHEDULE, AND

MILESTONES
(1)


SRI Proposal ERU 11
-
044 (Volume I)

31 March 2011

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USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.F.1

Technical Area 1: Continuous Sensing in Complex Fluid
(1)

The project schedule and key milestones
for this technical area
are shown in the Gantt chart below.

Key
milestones and costs associated with each third level WBS task are shown in the table below.


Continuous Sensing
Task Milestone & Cost T
able

Task

Title

Key Milestones

Year 1

Year 2

Year 3

Yea
r 4

1.1

Component
Development

Ring resonator development for 8
analytes (Month
XX
)

Sensor characterization study
(Month

XX
)

Microfluidic module development
(Month
XX
)

Demo 1 (Month
XX
)

$




2.1

Breadboard
System

Ring resonator development for 4

8
additional analytes (Month
XX
)

Characterization study (Month
XX
)

Breadboard module development

Demo 2 (Month
XX
)


$



3.1

Prototype
Development

Ring resonator development for full
analyte panel (Month
XX
)

Prototype
module development
(Month

XX
)

Demo 3 (Month
XX
)



$


SRI Proposal ERU 11
-
044 (Volume I)

31 March 2011

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USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.F.3

Technical Area 3: Intrinsic Separation from Complex Fluid
(1)



Task

Orgs
.

Year 1

Year 2

Year 3

Key Milestone
s

(Months After Start)

Phase I

3.1

3.5

SRI
(UC
Davis?)

add
columns
for
UCD?

line
for
each
task?





Delivery of MBL from Harvard (Mos 2, 6, 10)



Design review for magnetic bead separation device (Mo 3)



Conjugation of MBL and magnetic beads (Mo 6)



Construction of cytokine & bacteria separation component devices (Mo 6)



Demo of efficacy of M
BL against clinically relevant pathogens (Mo 9)



Delivery of cytokine & bacteria separation devices to integrator (Mo 9)



Task 3 Phase 1 demo (either beads or whole device) (Mo 11)



Task 3 Phase I report (Mo 12)

Phase II

II

3.1

3.5

SRI






Delivery of MBL
from Harvard (Mos 2, 6, 10)



Design review for magnetic bead separation device (Mo 3)



Conjugation of MBL and magnetic beads (Mo 6)



Construction of cytokine and bacteria separation breadboard devices (Mo 6)



Demo of efficacy of MBL against clinically relevant

pathogens (Mo 9)



Delivery of cytokine & bacteria separation breadboard devices to integrator
(Mo 9)



Task 3 Phase II demo (either beads or whole device) (Mo 11)



Task 3 Phase II report (Mo 12)

Phase III

III

3.1

3.5

SRI






Delivery of MBL from Harvard (Mos
2, 6, 10, 14, 16)



Design review for prototype magnetic bead separation device (Mo 3)



Conjugation of MBL and magnetic beads (Mo 6)



Construction of cytokine and bacteria separation prototype devices (Mo 6)



Initiation of efficacy experiments with animal testi
ng (Mo 6)



Demo of efficacy of MBL against clinically relevant pathogens (Mo 9)



Delivery of cytokine & bacteria separation breadboard devices to integrator
(Mo 9)



Task 3 Phase III demo (either beads or whole device) (Mo 11)



Identification of cytokine withdr
awal strategy for pig positive outcome (Mo 12)



Confirmation of efficacy of withdrawal strategy in pigs (Mo 16)

SRI Proposal ERU 11
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044 (Volume I)

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USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.F.4

Technical Area 4: Predictive Modeling
(1)



Task

Org
.

Year 1

Year 2

Year 3

Key Milestone
s

(Months After Start)

Phase I

4.1

4.6

SRI






Server deployed with secure access and initial clinical data imported (Mo 4)



Literature data integration complete.



Assessment scripts developed and applied to initial data set (Mo 5)



First level sepsis model framework developed (treating clinical data and

outcomes) * trained on data from selected clinical data set (Mo 8)



Model framework extended to second level (adding molecular profiles and
disease progression) and trained on clinical daa set augmented with
cytokine/mediate data (Mo 11)



Demo 1: Demonstrat
ion of a clinically relevant sepsis predictive model &
training algorithm performance on data sets from published literature (Mo 12)

Phase II

4.1

4.6

SRI






Complete mouse model based on published data sets and cytokine data from
project mouse study (Mo
16)



Model framework extended to support control (Mo 18)



Human model refined with additional clinical and molecular data (Mo 23)



Demo 2: Validation of sepsis predictive model using larger anonymous clinical
data sets and demonstrated performance in selectio
n of decision criteria and
feedback control to stabilize health & improve outcomes (Mo 24)

Phase III

4.1

4.6

SRI






Pig1 model trained to pig (Mo 30)



Pig 2 model learns response to drawdown (Mo 36)



Pig 3 model provides control decision choices (Mo 41)



Demo 3: Validation of the sepsis predictive model using data derived from
experimental animal studies and demonstrated performance in the selection of
decision criteria related to sepsis assessment and interventions (Mo 42)


SRI Proposal ERU 11
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044 (Volume I)

31 March 2011

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USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.F.5

Technical Area 5: System Integration
(1)





SRI Proposal ERU 11
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044 (Volume I)

31 March 2011

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USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

III.F.6

Technical Area 6: System Validation
(1)





USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
SRI INTERNATIONAL’S
PROPOSAL ERU 11
-
044 DATED 31 MARCH 2
011.


III.G.1

Continuous Sensing in Complex Fluid: Executive Summary

Main Goals

Continuously sense the presence of
pathogens and biomolecules in flowing blood,
blood components, and wound fluid at state
-
of
-
the
-
art detection limits.

App
roach

Use array of ring resonators, each
functionalized with a specific analyte binding
ligand, to detect specific blood components
with high sensitivity and specificity.

Expected Outcome

The proposed ring resonator sensor should
be capable of detecting do
zens of analytes in
blood or blood serum with high sensitivity in
near real time.

The device can be used to sample the input
and output blood streams in the DLT as well
as sample the effluent from the various
separation stages of the DLT.




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ION ON THE COVER OF
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044 DATED 31 MARCH 2
011.


III.G.1

Continuous Sensing in Complex Fluid
:
State of the Art

Competing sensing technologies such as cantilevers, surface Plasmon resonance
devices, nanowires, and interferometric approaches suffer from a number of
limitations relative to ring resonators.

Ring res
onators have been demonstrated to detect analytes at the pg/mL level and
can operate in highly multiplexed formats.

Label
-
F
ree Technology

Mechanical

SPR

Nanowire

Optical
Inter
-
ferometer

Silicon
Photonics
Ring
Resonators

Quartz

Cantilever

Carbon
Nanotube

Silicon
Nanowire

Single Molecule Capable
?

No

No

No

Yes

Yes

No

Yes

Concentration Sensitivity

High

High

Low

Low

Low

High

High

Mass Sensitivity

Low

Low
-
Med

Low





Low

High

Complex Media

Yes

Yes

Yes

No

No

Yes

Yes

Sample Prep

No

No

No

High

High

No

No

Throughput

Low

High

Med

High

High

Med

High

Cross

T
alk

Stress

Stress,
vibration

Vibration

Charge, salt
oxidation

Charge,
salt doping

Vibration

None

Cost

High

Low
?

Med
-
High

Low

Low

Low
-
Med

Low

Multiplexable

No

Yes

Marginal

Yes

Yes

Marginal

Yes

Maturity

Commercial

Commercial

Commercial

Research

Research

Commercial

Development

Clinical Use
?

No

Sometimes

No

No

No

Yes

Yes



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IIII.G.1

Continuous Sensing in Complex Fluid
:
Innovation

Key Advantages of the Ring Resonator Sensing Technology:



Label Free:

Requires no labeling technique (therefore no tagging or washing steps)



Sensitivity:
Demonstrated direct measurement of low pg/mL (comparable to ELISAs but with
results in minutes).



Dynamic Range:
In a representative assay system, direct detection demonstr
ated eight logs of
dynamic range. We have shown we can extend this further with a secondary detection
approach.



Rapid Time to Result:
Requires 2 to 10 min for a concentration readout.



Small Sensor Size:
The proprietary sensor design, with each ring 30 micr
ons in diameter,
enhances the effect of each individual molecule interaction hundreds of thousands of times.



Surface Preparation:
The pure glass surface is compatible with a diverse range of biological
assay systems. Sensor chip can be pre
-
functionalized u
sing standard conjugation chemistry
and micro
-
spotting techniques.



Multiplexing:
The first chip design (6 mm on a slide) carries 32 sensors, including 8 controls.
It

is possible to scale up to 40,000 sensors on a chip of the same dimensions.



Complex Media:
Readings for specific analyze in complex matrix (serum, nasal swab, etc.) are
obtained by employing a proprietary system to control for nonspecific binding activity.

No competing technology current available offers the combination of sensiti
vity, dynamic range,
multiplexing capability, or ability to operate in complex fluid media.


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III.G.1

Continuous Sensing in Complex Fluid
:

Risks and Technical Challenges

Demonstration of state of the art sensitivity in blood and/or blood serum

The sensor
must be able to detect clinically relevant levels of target analytes in a
complex medium. Testing in whole blood has not been evaluated and the presence
of cells in the blood will need to be characterized and factored into nonspecific
effects sensor and al
gorithm development.

Cross
-
reactivity between analytes in the panel and background proteins

The sensor must be able to detect each analyte of the panel independent of the
concentration of the other analytes or of background materials in the sample.
Antibod
ies will be selected initially to minimize cross
-
reactivity.

Sensitive detection of pathogens (bacteria and viruses)

We propose to detect bacteria and viruses using nonspecific ligands such as
mannose binding lectin, other lectins, and heparin, which will
nonspecifically bind
the cell walls of bacteria and the protein capsule of viruses. Detection of low
-
level
pathogens in blood may be a challenge given the blood volume throughput of the
DLT device.

Sensor lifetime in presence of biological fluids

The
sensor must operate in blood or serum without degrading or biofouling.


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011.


III.G.3

Intrinsic Separation from Complex Fluid
: Executive Summary

Main Goals



Broad
-
spectrum removal of bacteria and viruses



Selective removal of harmful cytokines/mediators and compl
ete removal of toxins



Selective high
-
throughput removal of harmful activated cells (ACs) while retaining
cells required to fight infection

Approach



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c慰瑵牥⁴漠a敭潶攠扡e瑥物愬⁣y瑯ti湥nⰠ
浥摩慴潲猬⁡湤⁴潸i湳
䍍味⤠慮搠
䅃A

Expected Outcome



䵥整⁡湤⁥c敥e⁰牯杲 洠m整物es



剥瑡R渠扥湥晩ci慬⁦畮 瑩潮映o浭畮攠
c敬ls⤠)桩l攠牥浯vi湧⁨慲浦畬⁢慣瑥物愬t
桡牭晵h⁃ 味Ⱐ慮T⁨慲浦畬⁡ 瑩v慴敤a
c敬ls



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JECT TO THE RESTRICT
ION ON THE COVER OF
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044 DATED 31 MARCH 2
011.


III.G.3

Intrinsic Separation from Complex Fluid
:
State of the Art

We have tailored our separation method to achieve best performance for each target:
cytokines, bacteria, and cells. Columns with blue headings show
SRI’s

approach.


Cytokine Removal

Bacteria Removal

Activated Cell Removal

Single

Cytokine

Removal

Size

Based

Removal

Affinity

Multi
-

Cytokine

Strain

Specific

Ligands

Micro
-
fluid
ics/Size

Specific

Class

Specific

Ligands

FACS/

MEMS
Gating

Micro
-

fluidics

Transient
Labeling

Speed

High

High

High

High

Low

High

Low

Moderate

High

Specificity

High

Low

High

High

Low

High

High

Low

High

Coverage

Low

High

High

Low

Moderate

High

High

Low

High

Benign

High

Low

High

High

Moderate

High

Moderate

Low

High



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011.


III.G.3

Intrinsic Separation from Complex Fluid
:
Innovation



Broad removal of bacteria and, possibly, viruses,
using an engineered form of
mannose binding lectin (MBL) as a capture agent with supplementation from SRI’s
Glycomics Laboratory and Toll
-
Like Receptor binding domains if needed.



Selective, adaptive affinity
-
based drawdown of cytokines and mediators.



Selective high
-
throughput removal of targeted cells on basis of cell type and cell
activation status using feedback from online sensing that identifies problem cell
subtypes.



A universal platform based on functionalized magnetic bead choreography (FMBC)
ca
pable of removing all different kinds of targets, either one at a time or multiple types
simultaneously. Furthermore, the architecture allows for complete removal of targets
or for controlled removal of only fractions of the target.

Metrics:



Phase I

50% wi
thdrawal of bacteria, CMTs, and ACs from whole blood



Phase II

90% withdrawal of bacteria, CMTs, and ACs from whole blood using the
breadboard system



Phase III

90% withdrawal of bacteria, CMTs, and ACs from an infected pig using our
prototype system


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011.


III.G.3

Intrinsic Separation from Complex Fluid
:

Risks and Technical Challenges

MBL may not bind to all bacteria species

Use improved MBLs from the Wyss Institute or supplement with other class
-
specific
ligands from SRI’s Glycomics Laboratory or others ba
sed on Toll
-
Like Receptors.

Flow rate limitations for magnetic bead binding to bacteria or CMTs

Increase magnetic bead concentrations, use hollow fiber filters or agarose beads,
or use electromagnetic to move magnetic beads to reduce diffusion reaction tim
es.

Magnetic beads may lyse RBCs at high flow rates

Use parallel separation or use hollow fiber filters.

Cells change functionally or interact during processing

Avoid targeting surface proteins that stimulate cells. Minimize cell processing time.

Antibody
off rate may limit throughput

Work with vendors to select antibodies with faster off rates and use screening
method for selection.


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ION ON THE COVER OF
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044 DATED 31 MARCH 2
011.


III.G.4

Predictive Modeling: Executive Summary

Main Goals

Computational models predictive of sepsis state and progression
suitable for
dialysis
-
like therapy

Approach

Development of a sepsis knowledge base

Development of multivariate statistical and multimodal graph
-
based predictive
models parameterized for training and adaptation

Expected Outcome

Trainable models, capable of
comparing prediction and measurement, and adapting
to patient
-
specific rates and ranges

Animal instantiations evaluated in test bed


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044 DATED 31 MARCH 2
011.


III.G.4

Predictive Modeling:
State of the Art

State of
the

Art

Existing models based on either large human studies with ma
ny uncontrolled
factors, mainly clinical data and a few with molecular measurements at one or two
time points, or small animal studies

Models are developed using



Univariate

and/or multivariate statistics to identify important factors



Differential equation
simulation models to predict progression or effects of
perturbation



Markov models of disease progression (history sensitive)

Limitations

Models are generally not tested on other data sets

Coarse grain measurements and time points


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III.G.4

Predictive Model
ing:
Innovation

What is New/Why They are Likely to be Successful

Combination of multiple modeling techniques

Based on large and dense data

Models that are adaptive and reactive

Short and long term prediction

Comparison of models trained on different
species (multiple animals, human)

Metrics and assessment Parameters

Statistical confidence measures

Granularity of time and variable ranges with high confidence


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011.


III.G.4

Predictive Modeling:
Risks and Technical Challenges

Risks

A key risk is identificatio
n of factors that support predictive models and can be
rapidly measured

This is being addressed by initially investigating a wide panel of sepsis mediators

Technical Challenges

Developing models that are robust to patient population variability

Animal mode
ls that can be retrained for human patients

Modifying training algorithms to be adaptive and reactive

Ensuring safe adaptation


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JECT TO THE RESTRICT
ION ON THE COVER OF
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044 DATED 31 MARCH 2
011.

III.G.5

System Integration
: Executive Summary

Main Goals



Integrate component technologies and modeling knowledge from Tasks 1

4
to
create a full DLT system ready for Phase IV validation



Demonstrate a treatment for sepsis using the DLT system

Approach



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瑯⁡tl潷⁣潮o畲牥湴n
摥d敬潰浥o琠潦⁳yst敭⁡湤
c潭灯o敮琠瑥e桮潬潧o敳⁦牯洠
卒䤠潲⁴桩牤r灡牴y⁤敶敬潰敲o



䍯浰牥C敮eiv攠慮e浡m⁥ 灥物
-
浥湴m⁴漠敶慬畡瑥⁣潭灯o敮琠
慮搠ays瑥洠灥牦r牭慮r攠w桩l攠


informing the predictive model algorithms

designed to control the machine

Expected Outcome



Meet and exceed program metrics



Completion of working DLT prototype system

ready for Phase IV validation


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JECT TO THE RESTRICT
ION ON THE COVER OF
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044 DATED 31 MARCH 2
011.


III.G.5

System Integration
:
State of the Art


Separation
of

Blood
Components

Removal
of

Small
Molecules

Removal of
Pathogens

Removal of

Cell
Populations

Selective
Controlled
Drawdown
of

Cytokines

SRI DLT

Yes

Yes

Yes

Yes

Yes

Blood
purification
using hollow
fiber filters

No

Yes

No

No

No

Plasma
-
pheresis

Yes

Yes

Depends on
separation
fraction removed

Not typical, but entire
separation fractions
may be removed

No








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JECT TO THE RESTRICT
ION ON THE COVER OF
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044 DATED 31 MARCH 2
011.


III.G.5

System Integration
:

Innovation



Approach that allows
rapid

removal of pathogens and
selective

removal of cytokines,
mediators, and deleterious cells that are specifically responsible for clinical
manifestations of sepsis while
preserving

plasma levels of beneficial biomolecules



Open and
modular architecture

that allows plug
-
and
-
play components for testing and
evaluation with baseline design



Adaptable

controller that allows closed loop removal of biomolecules based on the
state of the patient and biomolecules sensor measurements



Concurrent

design process to allow parallel development of system and individual
components



Regulatory strategy to achieve basic usable product that is safe and effective with an
architecture that can support advanced future capabilities



Comprehensive animal experim
ents to evaluate component and system performance
while informing the predictive model algorithms designed to control the machine



In
-
house infectious disease expertise and collaborations with thought leaders in sepsis



Collaborative development with users a
nd military personnel to facilitate transition of
the technology starting with clinical trials in relevant DoD centers



Active engagement of commercial partner in the apheresis business


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JECT TO THE RESTRICT
ION ON THE COVER OF
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044 DATED 31 MARCH 2
011.


III.G.5

System Integration
:
Risks and Technical Challenges

Technical
Risk

Mitigation

Performance under target for pathogen/
biomolecules removal components

Leave margin to increase flow rate

Sensor performance not adequate

Make off
-
line measurements

Animal models not compatible with
extracorporeal volumes required in
benchtop/breadboard

Expand options for animal models; scale
down certain components; autologous
blood circuit priming

Efficacy in one pig model is not
reproduced in a second model with a
different pathogen

Explore alternative cytokine/mediator
drawdown co
nfiguration

Approaches require anticoagulant

Use regional anticoagulant

Safety concerns on removal of certain
cytokines or cells

Revise cytokine and cell removal profile
if necessary



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JECT TO THE RESTRICT
ION ON THE COVER OF
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011.


III.G.6

System Validation
: Executive Summary

Main Goals



Ensure the
prototype DLT device functions as expected at an acceptable level of risk



Prepare Investigational Device Exemption (IDE) application to FDA

Approach



噡Vi摡瑩潮⁷i瑨⁡湩浡m潤敬s



噡Vi摡瑥⁳ys瑥洠s慦整y



噡Vi摡瑥⁳ys瑥洠敦晩c慣y



噡Vi摡瑥⁳潦瑷a牥⁦畮 瑩潮



噡Vi摡瑥⁳ys瑥洠灥牦潲p慮ae

Expected Outcome



䵥整⁡湤⁥c敥e⁰牯杲 洠m整物es



䑌吠Dys瑥洠ts⁶慬i摡瑥d



䥄䔠慰灬ic慴a潮⁲敡oy⁦ 爠獵扭issi潮


Development Process
Design
Pre
-
Clinical Development
Clinical Development
FDA Filing Approval
Update Risk
Analysis
Develop Risk
Mitigation
Strategy
Final System
Design
Substantially
Equivalent
?
Low Risk
?
File
510
k
Device Cleared
Yes
No
Additional
Information
Requested
?
Compile additional
data
NO
YES
File De Novo
Application
File PMA
Application
YES
NO
Final Pre
-
IDE
Meeting
Establish Device
Safety
Study design
,
endpoint
,
analysis
agreement
?
Execute Study
Results validate
medical utility
?
Significant
risk
?
IRB approval
IDE approved
?
Submit IDE
NO
YES
YES
NO
YES
Address concerns
NO
YES
Risk as low as
reasonably possible
?
Potential benefits
outweigh risks
?
YES
Yes
YES
NO
NO
No
NO
Validate
Conformance to
PRS
(
includes
Animal Studies
Validation
Success
?
YES
NO
STOP
-

reevaluation of
product required
Concept
Development
Z
1
Build
Redesign Protocol
NO
Validate Software
Verification
Studies
c
Product
Requirements
Specification
(
PRS
)
Clinical Data
Required
?
Yes
No
Design
Requirements
Specifications
Design
Requirements
Specifications
Design
Requirements
Specifications
Human Factors
Analysis
Risk Analysis
Perform
Design
Activities
DR
1
DR
2
DR
4
DR
3
c
Supporting
Animal
Studies
Year
1
Year
2
,
3
Year
4
,
5
Post
-
Project
Primary Development Path
Secondary Development Path

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011.


III.G.6

System Validation
:
State of the Art


Separation
of

Blood
Components

Removal
of

Small
Molecules

Removal of

Pathogens

Removal of

Cell
Populations

Selective
Controlled
Drawdown
of

Cytokines

SRI DLT

Yes

Yes

Yes

Yes

Yes

Blood
purification
using hollow
fiber filters

No

Yes

No

No

No

Plasma
-
pheresis

Yes

Yes

Depends on
separation
fraction removed

Not typical, but
entire
separation fractions
may be removed

No



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JECT TO THE RESTRICT
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011.


III.G.6

System Validation
:

Innovation



Animal facilities with capability to
handle infectious disease models for small animals,
pigs, and nonhuman primates



Extensive pre
-
clinical experience testing with
animal models by a team of
veterinarians, toxicologists, and animal care specialists



Infectious disease clinical specialists



Collaborations with sepsis thought
-
leaders in military and civilian medical facilities



Relationships with therapeutic apheresis mar
ket leaders prepared to support
validation and market introduction of the device designed



Risk mitigation strategy for regulatory and market introduction based on stepped
approach to increasingly sophisticated generations of the system



Extensive experience

in commercialization and licensing of complex technologies in
the medical domain


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III.G.6

System Validation
:
Risks and Technical Challenges

Technical or Programmatic Risk

Mitigation

Technical


System fails to pass one or more validation
tests

Analyze
failure, modify system documentation
or test protocol per design control process,
follow corrective procedures, retest the system

Programmatic


The Z1 build of the system is not available at
the beginning of the validation phase

Postpone start of validat
ion phase

Validation test documentation not available at
beginning of validation phase

Draft and review test documentation prior to
beginning of the validation phase

IACUC protocols not approved per program
schedule

Animal protocols will be developed
with
attention to humane treatment and animal
welfare

Animal efficacy in pigs is not replicated in
nonhuman primates

Other promising device configurations in pigs
(i.e., alternative mediator drawdown strategies)
can be evaluated in additional NHP studies


SRI Proposal ERU 11
-
044 (Volume I)

31 March 2011

87

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ION ON THE COVER OF
THIS PROPOSAL.

SECTION IV: ADDITION
AL INFORMATION

IV.A

BIBLIOGRAPHY

Section II.A Reference:

1.

Stegmayr, 2008

Section
III.B.4 References:

1.

Bing Liu, Jing Zhang, Pei Yi Tan, David Hsu, Anna M. Blom, Benjamin Leong, Sunil Sethi, Bow
Ho, Jeak Ling Ding, and P. S. Thiagarajan. 2001. A Computational and Experimental Study of the
Regulatory Mechanisms of the Complement System
. PLoS Computational Biology January, Volume
7, Issue 1. (
Thiang1)

2.

Bing Liu, David Hsu, and P.S. Thiagarajan. 2011. Probabilistic approximations of ODEs based bio
-
pathway dynamics. Theoretical Computer Science, doi:10.1016/j.tcs.2011.01.021.
(Thiang2)

3
.

C. E. Garcia, D. M. Prett, and M. Morari. 1989. Model predictive control: theory and practice.
Journal Automatica Volume 25, Issue 3. (
Garcia, 1989
)

4.

Systemic Inflammatory Response and Progression to Severe Sepsis in Critically Ill Infected Patients.
C
orinne Alberti, Christian Brun
-
Buisson, Sylvie Chevret, Massimo Antonelli, Sergey V. Goodman,
Claudio Martin, Rui Moreno, Ana R. Ochagavia, Mark Palazzo, Karl Werdan and Jean Roger Le
Gall. Am J Respir Crit Care Med Vol 171. pp 461‚
Äì
468, 2005. (Alberti 20
05)

5.

Fernando A. Bozza, Jorge I. Salluh, Andr
é

M Japiassu1, Marcio Soares, Edson F. Assis, Rachel N
Gomes, Marcelo T Bozza, Hugo C. Castro
-
Faria
-
Neto and Patr
í
cia T. Bozza. 2007. Cytokine
profiles as markers of disease severity in sepsis: a multiplex a
nalysis. Critical Care, Vol 11, No 2.
(
Bozza, 2007
)

6.

Y. Vodovotz, C. C. Chow, J. Bartels, C. Lagoa, J. M. Prince, R. M. Levy, R. Kumar, J. Day, J.
Rubin, G. Constantine,T. R. Billiar, M. P. Fink, and
Clermont G. Shock
. 2006. In silico models of
acute inf
lammation in animals. Sep;26(3):235
-
44. (
Clemmmont, Vodovotz, 2006 (
one or two
refs?)

should be Clermont)

7.

M. Sigfrido Rangel
-
Frausto, Didier Pittet, Taekyu Hwang, Robert F. Woolson, and Richard P.
Wenzel. 1998. The Dynamics of Disease Progression in Sep
sis: Markov Modeling Describing the
Natural History and the Likely Impact of Effective Antisepsis Agents. Clinical Infectious Diseases,
1998;27:185‚
Äì
90. (
Rangel
-
Frausto
1998
)

8.


Charalambos A. Gogos, Eugenia Drosou, Harry P. Bassaris, and Athanassios Skoutelis. Pro
-

versus
Anti
-
Inflammatory Cytokine Profile in Patients with Severe Sepsis: A Marker for Prognosis and
Future Therapeutic Options. 2000. The Journal of Infectious Disea
ses Vol. 181, No. 1 (pp. 176

180). (
Gogos 2000
)

9.

Sergey M Zuev, Stephen F Kingsmore and Damian DG Gessler.Sepsis progression and outcome: a
dynamical model. 2006. Theoretical Biology and Medical Modelling, 3:8doi:10.1186/1742
-
4682
-
3
-
8.
(Zuev, 2006
)

10.

G
orkem Saka, Jennifer Kreke, Andrew J. Schaefer, Derek C. Angus, and Mark S. Roberts. 2007.
Predicting Disease Progression Using Dynamic Simulation in Pneumonia
-
Related Sepsis Critical
Care 2007, 11:R65 (doi:10.1186/cc5942). (
Saka, 2007
)

SRI Proposal ERU 11
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044 (Volume I)

31 March 2011

88

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ION ON THE COVER OF
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Section III.B.5 Re
ference:

1.

Sauer et al. 2009

Section III.B.6 Reference:

1.

Kaneko
et al., 2003

2.

Redl et al., 2005

Section III.C. 3 References:

1.

P. S. Williams, M. Zborowski, and J. J. Chalmers. 1999. Flow rate optimization for the quadrupole
magnetic cell sorter. Ana
lytical chemistry 71, 3799
-
3807.

2
.

L. R. Antonelli,
W. O. Dutra, R. P. Almeida, O. Bacellar, E. M. Carvalho, and K. J. Gollob. 2005.
Activated inflammatory T cells correlate with lesion size in human cutaneous leishmaniasis.
Immunol Lett 101:226
-
230
.

3
.

R
. L. Bottrel,
W. O. Dutra, F. A. Martins, B. Gontijo, E. Carvalho, M. Barral
-
Netto, A.

Barral, R. P.
Almeida, W. Mayrink, R. Locksley, and K. J. Gollob. 2001. Flow cytometric determination of
cellular sources and frequencies of key cytokine
-
producing lymph
ocytes directed against
recombinant LACK and soluble Leishmania antigen in human cutaneous leishmaniasis. Infect
Immun 69:3232
-
3239.

4
.

R. P. Costa,
K. J. Gollob, P. R. Machado, O. A. Bacellar, R. P. Almeida, A. Barral, M.

Barral
-
Netto,
E. M. Carvalho, and

W. O. Dutra. 2003. Adhesion molecule expression patterns indicate activation
and recruitment of CD4+ T cells from the lymph node to the peripheral blood of early cutaneous
leishmaniasis patients. Immunol Lett 90:155
-
159.

5
.

W. O. Dutra,
R.
Correa
-
Oliveira, D. Dunne, L. F. Cecchini, L. Fraga, M. Roberts, A. M. Soares
-
Silveira, M. Webster, H. Yssel, and K. J. Gollob. 2002. Polarized Th2 like cells, in the absence of
Th0 cells, are responsible for lymphocyte produced IL
-
4 in high IgE
-
producer s
chistosomiasis
patients. BMC Immunol 3:8.

6
.

S. T. Gaze,
W. O. Dutra, M. Lessa, H. Lessa, L. H. Guimaraes, A. R. Jesus, L. P. Carvalho, P.
Machado, E. M. Carvalho, and K. J. Gollob. 2006. Mucosal leishmaniasis patients display an
activated inflammatory T
-
c
ell phenotype associated with a nonbalanced monocyte population. Scand
J Immunol 63:70
-
78.

7
.

E.
Rocha
-
Vieira
,
E. Ferreira, P. Vianna, D. R. De Faria, S. T. Gaze, W. O. Dutra, and K. J. Gollob.
2003. Histopathological outcome of Leishmania major
-
infected B
ALB/c mice is improved by oral
treatment with N
-
acetyl
-
l
-
cysteine. Immunology 108:401
-
408.

8
.

P. E. Souza,
M. O. Rocha, E. Rocha
-
Vieira, C. A. Menezes, A. C. Chaves, K. J. Gollob, and W. O.
Dutra. 2004. Monocytes from patients with indeterminate and cardia
c forms of Chagas' disease
display distinct phenotypic and functional characteristics associated with morbidity. Infect Immun
72:5283
-
5291.

9
.

K. C. Torres,
L. R. Antonelli, A. L. Souza, M. M. Teixeira, W. O. Dutra, and K. J. Gollob. 2005.
Norepinephrine,
dopamine and dexamethasone modulate discrete leukocyte subpopulations and
cytokine profiles from human PBMC. J Neuroimmunol 166:144
-
157.

10
.

F. N. Villani,
M. O. Rocha, C. Nunes Mdo, L. R. Antonelli, L. M. Magalhaes, J. S. dos Santos, K. J.
Gollob, and W.
O. Dutra. 2010. Trypanosoma cruzi
-
induced activation of functionally distinct
alphabeta and gammadelta CD4
-

CD8
-

T cells in individ
uals with polar forms of Chagas’

disease.
Infect Immun 78:4421
-
4430.

SRI Proposal ERU 11
-
044 (Volume I)

31 March 2011

89

USE OR DISCLOSURE OF

PROPOSAL DATA IS SUB
JECT TO THE RESTRICT
ION ON THE COVER OF
THIS PROPOSAL.

IV.B

RELEVANT PAPERS

The following papers are included

with this submission:

1.

2.

3.