Granted Patent
B2
US 12,440,837 · App. 19/177,401 · Granted Oct 14, 2025
Devices and methods for analyzing biological samples
Inventors:
Tarun Kumar Khurana (Fremont, CA); Ali Agah (Redwood City, CA); Yir-Shyuan Wu (Albany, CA); Filiz Gorpe Yasar (Redwood City, CA)
Assignee:
CELLANOME, INC.
B01L3/502715B01L3/502707B01L3/502761C12Q1/6869C12Q1/6874G01N33/54386G01N33/6842B01L2200/0647B01L2200/12B01L2300/0663B01L2300/0883B01L2300/12B01L2300/163B01L2300/18C12Q2600/158G01N2570/00
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Abstract
Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.
Claims (33)
1. A method, comprising:
(a) introducing a plurality of cells into a fluidic device;
(b) introducing one or more polymer precursors into the fluidic device; and
(c) using a virtual photomask to selectively apply light to the fluidic device to polymerize the one or more polymer precursors, thereby selectively encapsulating a cell of the plurality of cells in the fluidic device.
2. The method of claim 1 , wherein the virtual photomask is generated from a spatial light modulator (SLM).
3. The method of claim 2 , wherein the SLM is a digital micromirror device (DMD), and wherein the DMD directs a unit of energy generated from an energy source to a discrete area of the fluidic device.
4. The method of claim 1 , wherein in (c), the cell is selectively encapsulated within a chamber comprising one or more polymer matrix walls.
5. The method of claim 4 , further comprising selectively encapsulating one or more additional cells of the plurality of cells in an additional chamber comprising one or more additional polymer matrix walls.
6. The method of claim 5 , wherein the cell and the one or more additional cells are selectively encapsulated simultaneously.
7. The method of claim 4 , wherein the one or more polymer matrix walls extend from a first surface of the fluidic device to a second surface opposite of the first surface, thereby forming an interior of the chamber, wherein the interior of the chamber comprises the cell.
8. The method of claim 1 , further comprising, subsequent to (c), processing a biological material of the cell.
9. The method of claim 8 , further comprising lysing the cell to obtain the biological material of the cell.
10. The method of claim 8 , wherein the biological material is released from the cell upon interaction with a reagent.
11. The method of claim 8 , wherein the biological material comprises messenger ribonucleic acids (mRNAs).
12. The method of claim 11 , wherein the method further comprises capturing the mRNAs with one or more capture oligonucleotides, wherein the one or more capture oligonucleotides are coupled to a surface of the fluidic device, thereby obtaining captured mRNAs.
13. The method of claim 12 , wherein the one or more capture oligonucleotides are selectively encapsulated with the cell.
14. The method of claim 12 , wherein the one or more capture oligonucleotides each comprise a barcode, wherein a sequence of the barcode indicates a position within the fluidic device.
15. The method of claim 12 , further comprising loading the fluidic device with reverse transcription reagents to produce complementary deoxyribonucleic acids (cDNAs) from the captured mRNAs.
16. The method of claim 15 , further comprising sequencing the cDNAs or derivatives thereof.
17. The method of claim 16 , wherein the cDNAs or derivatives thereof are removed from the fluidic device prior to the sequencing.
18. The method of claim 1 , further comprising releasing one or more proteins from the cell.
19. The method of claim 18 , wherein the one or more proteins are secreted from the cell.
20. The method of claim 18 , wherein the one or more proteins comprise a cytokine.
21. The method of claim 18 , wherein the one or more proteins are captured by an antibody located on a portion of the fluidic device.
22. The method of claim 21 , wherein the antibody is selectively encapsulated with the cell.
23. The method of claim 18 , wherein the one or more proteins are captured by an antibody, wherein the antibody is coupled to a bead.
24. The method of claim 23 , wherein the bead is selectively encapsulated with the cell.
25. The method of claim 1 , wherein the cell is selectively encapsulated with one or more antibodies specific for surface proteins whose relative expression permits identification of the cell.
26. The method of claim 25 , further comprising releasing the surface proteins from the cell, thereby obtaining one or more antibody-cell surface protein complexes.
27. The method of claim 26 , wherein the one or more antibody-cell surface protein complexes are captured by one or more capture oligonucleotides located on a surface of the fluidic device.
28. The method of claim 25 , wherein the one or more antibodies are selected to identify the cell as a CD8+T cell, a monocyte, a CD4+T cell, an NK cells, a DC cell, or a B cell.
29. The method of claim 1 , wherein in (c), an additional cell of the plurality of cells is selectively encapsulated with the cell.
30. The method of claim 29 , further comprising analyzing an interaction between the cell and the additional cell.
Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Jul 22, 2025
From: KHURANA, TARUN KUMAR; AGAH, ALI; WU, YIR-SHYUAN; YASAR, FILIZ GORPE
To: CELLANOME, INC.
Reel/Frame 071796/0833 →
Continuity (7)
Continuation
PCTUS2022011720
· Jan 7, 2022
Provisional Application
63253500
· Oct 7, 2021
Provisional Application
63135463
· Jan 8, 2021
References Cited (376)
US 4683195A
· Mullis et al.
· 1987
[cited by applicant]
US 4683202A
· Mullis
· 1987
[cited by applicant]
US 4800159A
· Mullis et al.
· 1989
[cited by applicant]
US 4942124A
· Church
· 1990
[cited by applicant]
US 4965188A
· Mullis et al.
· 1990
[cited by applicant]
US 5126022A
· Soane et al.
· 1992
[cited by applicant]
US 5168038A
· Tecott et al.
· 1992
[cited by applicant]
US 5210015A
· Gelfand et al.
· 1993
[cited by applicant]
US 5367066A
· Urdea et al.
· 1994
[cited by applicant]
US 5399491A
· Kacian et al.
· 1995
[cited by applicant]
US 5498392A
· Wilding et al.
· 1996
[cited by applicant]
US 5587128A
· Wilding et al.
· 1996
[cited by applicant]
US 5700642A
· Monforte et al.
· 1997
[cited by applicant]
US 5739386A
· Holmes
· 1998
[cited by applicant]
US 5830655A
· Monforte et al.
· 1998
[cited by applicant]
US 5854033A
· Lizardi
· 1998
[cited by applicant]
US 5858195A
· Ramsey
· 1999
[cited by applicant]
US 5925517A
· Tyagi et al.
· 1999
[cited by applicant]
US 6001229A
· Ramsey
· 1999
[cited by applicant]
US 6010607A
· Ramsey
· 2000
[cited by applicant]
US 6033546A
· Ramsey
· 2000
[cited by applicant]
US 6054034A
· Soane et al.
· 2000
[cited by applicant]
US 6060288A
· Adams et al.
· 2000
[cited by applicant]
US 6090592A
· Adams et al.
· 2000
[cited by applicant]
US 6174670B1
· Wittwer et al.
· 2001
[cited by applicant]
US 6312134B1
· Jain et al.
· 2001
[cited by applicant]
US 6399952B1
· Maher et al.
· 2002
[cited by applicant]
US 6514706B1
· Von Kalle et al.
· 2003
[cited by applicant]
US 6569627B2
· Wittwer et al.
· 2003
[cited by applicant]
US 6613525B2
· Nelson et al.
· 2003
[cited by applicant]
US 6787308B2
· Balasubramanian et al.
· 2004
[cited by applicant]
US 6960437B2
· Enzelberger et al.
· 2005
[cited by applicant]
US 7097809B2
· Van et al.
· 2006
[cited by applicant]
US 7276381B2
· Kitagawa
· 2007
[cited by applicant]
US 7425431B2
· Church et al.
· 2008
[cited by applicant]
US 7771949B2
· Kramer
· 2010
[cited by applicant]
US 7824854B2
· Arai et al.
· 2010
[cited by applicant]
US 8173080B2
· Lebl et al.
· 2012
[cited by applicant]
US 8778849B2
· Bowen et al.
· 2014
[cited by applicant]
US 8822647B2
· Jensen
· 2014
[cited by applicant]
US 8900828B2
· Smith et al.
· 2014
[cited by applicant]
US 8906684B2
· Bhatia et al.
· 2014
[cited by applicant]
US 8921073B2
· Reed et al.
· 2014
[cited by applicant]
US 9057097B2
· Piepenburg et al.
· 2015
[cited by applicant]
US 9068155B2
· Allbritton et al.
· 2015
[cited by applicant]
US 9169513B2
· Shen et al.
· 2015
[cited by applicant]
US 9367049B2
· Jariwala et al.
· 2016
[cited by applicant]
US 9476080B2
· Li et al.
· 2016
[cited by applicant]
US 9487745B2
· Wang et al.
· 2016
[cited by applicant]
US 9512422B2
· Barnard et al.
· 2016
[cited by applicant]
US 9561622B2
· Das et al.
· 2017
[cited by applicant]
US 9593365B2
· Frisen et al.
· 2017
[cited by applicant]
US 9631092B2
· Bowman et al.
· 2017
[cited by applicant]
US 9758578B2
· Fujino et al.
· 2017
[cited by applicant]
US 9765291B2
· Allbritton et al.
· 2017
[cited by applicant]
US 9963666B2
· Allbritton et al.
· 2018
[cited by applicant]
US 20030096239A1
· Gunderson et al.
· 2003
[cited by applicant]
US 20030175824A1
· Pishko et al.
· 2003
[cited by applicant]
US 20030186226A1
· Brennan et al.
· 2003
[cited by applicant]
US 20040106728A1
· McGall et al.
· 2004
[cited by applicant]
US 20040219214A1
· Gravett et al.
· 2004
[cited by applicant]
US 20050282156A1
· Rava et al.
· 2005
[cited by applicant]
US 20100292931A1
· Wang et al.
· 2010
[cited by applicant]
US 20120202263A1
· Blakely et al.
· 2012
[cited by applicant]
US 20120270209A1
· Shah et al.
· 2012
[cited by applicant]
US 20150159204A1
· Drmanac et al.
· 2015
[cited by applicant]
US 20160375143A1
· Gunatillake et al.
· 2016
[cited by applicant]
US 20190062835A1
· López Escámez
· 2019
[cited by examiner]
US 20200080046A1
· Gebhart et al.
· 2020
[cited by applicant]
US 20200362334A1
· Regev et al.
· 2020
[cited by applicant]
US 20200399428A1
· Kleine-Brüggeney et al.
· 2020
[cited by applicant]
US 20210079386A1
· Kaper et al.
· 2021
[cited by applicant]
US 20220025447A1
· Tentori et al.
· 2022
[cited by applicant]
US 20220033893A1
· Lan et al.
· 2022
[cited by applicant]
US 20220034867A1
· Butler et al.
· 2022
[cited by applicant]
US 20220219170A1
· Khurana et al.
· 2022
[cited by applicant]
US 20230001413A1
· Khurana et al.
· 2023
[cited by applicant]
EP 3450471A1
· 2019
[cited by applicant]
EP 3145689B1
· 2020
[cited by applicant]
EP 3450471B1
· 2020
[cited by applicant]
EP 3836887B1
· 2024
[cited by applicant]
GB 2315700A
· 1998
[cited by applicant]
JP H04262799A
· 1992
[cited by applicant]
KR 20210103010A
· 2021
[cited by applicant]
NL 2017834
· 2018
[cited by applicant]
WO WO9919717A1
· 1999
[cited by applicant]
WO WO0224322A2
· 2002
[cited by applicant]
WO WO2004006840A2
· 2004
[cited by applicant]
WO WO2005074569A2
· 2005
[cited by applicant]
WO WO2006125458A1
· 2006
[cited by applicant]
WO WO2010132795A2
· 2010
[cited by applicant]
WO WO2014031997A1
· 2014
[cited by applicant]
WO WO2015010019A1
· 2015
[cited by applicant]
WO WO2015164212A1
· 2015
[cited by applicant]
WO WO2015179572A1
· 2015
[cited by applicant]
WO WO2017048993A1
· 2017
[cited by applicant]
WO WO2017075265A1
· 2017
[cited by applicant]
WO WO2018097715A1
· 2018
[cited by applicant]
WO WO2018172726A1
· 2018
[cited by applicant]
WO WO2019028047A1
· 2019
[cited by applicant]
WO WO2019028166A1
· 2019
[cited by applicant]
WO WO2019157529A1
· 2019
[cited by applicant]
WO WO2019203728A1
· 2019
[cited by applicant]
WO WO2020047002A1
· 2020
[cited by applicant]
WO WO2020120442A2
· 2020
[cited by applicant]
WO WO2020190509A1
· 2020
[cited by applicant]
WO WO2020255108A1
· 2020
[cited by applicant]
WO WO2021108499A1
· 2021
[cited by applicant]
WO WO2021122579A1
· 2021
[cited by applicant]
WO WO2022013094A1
· 2022
[cited by applicant]
WO WO2022015600A2
· 2022
[cited by applicant]
WO WO2022096294A2
· 2022
[cited by applicant]
WO WO2022150659
· 2022
[cited by applicant]
WO WO2022261507
· 2022
[cited by applicant]
WO WO2023183327A1
· 2023
[cited by applicant]
WO WO2023196603A1
· 2023
[cited by applicant]
WO WO2023225366A1
· 2023
[cited by applicant]
WO WO2023240207A1
· 2023
[cited by applicant]
WO WO2024020398A1
· 2024
[cited by applicant]
WO WO2024092056A1
· 2024
[cited by applicant]
WO WO2024145393A1
· 2024
[cited by applicant]
Adessi, Celine, et al. Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic acids research 28(20):E87, 1-8 (2000).
[cited by applicant]
Albrecht et al., “Photo- and electropatterning of hydrogel-encapsulated living cell arrays,” LabChip, 5: 111-118 (2005).
[cited by applicant]
Allen, Elizabeth S. et al. Autologous lymphapheresis for the production of chimeric antigen receptor T cells. Transfusion 57(5):1133-1141 (2017).
[cited by applicant]
Anderson, Rhona. Multiplex fluorescence in situ hybridization (M-FISH). Fluorescence in situ Hybridization (FISH) Protocols and Applications 659:83-97 (2010).
[cited by applicant]
Annabi, Nasim et al. Controlling the porosity and microarchitecture of hydrogels for tissue engineering. Tissue Engineering: Part B 16(4):371-383 (2010).
[cited by applicant]
Attayek, Peter J. et al. Array-based platform to select, release, and capture Epstein-barr virus- infected cells based on intercellular adhesion. Analytical chemistry 87(24):12281-12289 (2015).
[cited by applicant]
Attayek, Peter J. et al. Identification and isolation of antigen-specific cytotoxic T lymphocytes with an automated microraft sorting system. Integrative Biology 8(12):1208-1220 (2016).
[cited by applicant]
Barrett, David M. et al. Chimeric Antigen Receptor Therapy For Cancer. Annual Review of Medicine 65:333-347 (2014). Published online Nov. 20, 2013.
[cited by applicant]
Basu, Swarna, and Campagnola, Paul J. Enzymatic activity of alkaline phosphatase inside protein and polymer structures fabricated via multiphoton excitation. Biomacromolecules, American Chemical Society 5(2):572-579 (20…
[cited by applicant]
Bayani, Jane, and Jeremy A Squire. Unit 22.4: Fluorescence in situ Hybridization (FISH). Current Protocols in Cell Biology Supplement 23:22.4, 1-52 (2004).
[cited by applicant]
Biasco, Luca et al. Analyzing the Genotoxicity of Retroviral Vectors in Hematopoietic Cell Gene Therapy. Molecular Therapy Methods & Clinical Development 8:21-30 (2017).
[cited by applicant]
Bose, Sayantan. et al. Scalable Microfluidics for Single-cell RNA Printing and Sequencing. Genome Biology 16(1):120, 1-16 (2015).
[cited by applicant]
Bradford, Jolene A, and Gayle M. Buller. Dead Cell Stains In Flow Cytometry: A Comprehensive Analysis. Poster presented at Molecular Probes. p. 1 (2009).
[cited by applicant]
Burdick et al., “Moving from static to dynamic complexity in hydrogel design,” Nature Comm., 3: 1269 (Dec. 11, 2012).
[cited by applicant]
Caliari, Steven R. et al. A Practical Guide to Hydrogels for Cell Culture. Nature Methods 13(5):405-414 (2016).
[cited by applicant]
Cha et al, “Structural reinforcement of cell-laden hydrogels with microfabricated three dimensional scaffolds,” Biomaterial Science, 2(5): 703-709 (2014).
[cited by applicant]
Chava, Suresh. et al. Measurement of Natural Killer Cell-Mediated Cytotoxicity and Migration in the Context of Hepatic Tumor Cells. Journal of Visualized Experiments 156:e60714, 1-7 (2020).
[cited by applicant]
Chen, A. et al. Vector copy number quality control testing for CAR T-cells: critical validation parameters. Cytotherapy 22(5):S142, 1-1 (2020).
[cited by applicant]
Chen, Ao. et al. Spatiotemporal Transcriptomic Atlas of Mouse Organogenesis2 using DNA Nanoball Patterned Arrays. bioRxiv :1-75 (2021).
[cited by applicant]
Cheng, Jing, and Larry J. Kricka. Biochip Technology. CRC Press (2001).
[cited by applicant]
Cho, Chun-Seaok et al. Seq-Scope: Submicrometer-resolution Spatial Transcriptomics for Single Cell and Subcellular Studies. bioRxiv :1-50 (2021).
[cited by applicant]
Choi, Jane Ru et al. Recent advances in photo-crosslinkable hydrogels for biomedical applications. BioTechniques 66(1):40-53 (2019).
[cited by applicant]
Cornetta, Kenneth et al. Meeting FDA Guidance recommendations for replication-competent virus and insertional oncogenesis testing. Molecular Therapy Methods & Clinical Development 28:28-39 (2022).
[cited by applicant]
Cortes-Llanos, Belen. et al. A technology of a different sort: microraft arrays. Lab on a Chip 21(17):3204-3218 (2021).
[cited by applicant]
Cui, X F. et al. Single-sperm typing: determination of genetic distance between the G gamma-globin and parathyroid hormone loci by using the polymerase chain reaction and allele-specific oligomers. Proceedings of the Na…
[cited by applicant]
Curley et al., “Fabrication of micropatterned hydrogels for neural culture systems using dynamic mask projection photolithography,” J. Visualized Experiments, 48: e2636 (2011).
[cited by applicant]
Deforest, Cole A. and Anseth, Kristi S. Cytocompatible Click-based Hydrogels with Dynamically-Tunable Properties Through Orthogonal Photoconjugation and Photocleavage Reactions. Nature Chemistry. 3(12):925-931 (2011).
[cited by applicant]
Deleye, Lieselot. et al. Performance of four modern whole genome amplification methods for copy number variant detection in single cells. Scientific Reports 7:3422, 1-9 (2017).
[cited by applicant]
Deleye, Lieselot et al. Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method. Scientific Reports 5:11711, 1-13 (2015).
[cited by applicant]
D'Eramo et al., “Microfluidic actuators based on temperature-responsive hydrogels,” Microsystems & Nanoengineering, 4: 17069 (2018).
[cited by applicant]
Desfarges, Sébastien, and Angela Ciuffi. Retroviral Integration Site Selection. Viruses 2(1):111-130 (2010).
[cited by applicant]
Ding et al, “Single-cell RNA sequencing in breast cancer: understanding tumor heterogeneity and paving roads to individualized therapy,” Cancer Communications, 40: 329-344 (2020).
[cited by applicant]
Dittrich, Petra, and Norbert Jakubowski. Current trends in single cell analysis. Analytical and Bioanalytical Chemistry 406(27):6957-6961 (2014).
[cited by applicant]
Drury, Jeanie L, and David J Mooney et al. Hydrogels for Tissue Engineering: Scaffold Design Variables and Applications. Biomaterials 24(24):4337-4351 (2003).
[cited by applicant]
Edelman, Gerald M, and Joseph A. Gally. Degeneracy and complexity in biological systems. Proc Natl Acad Sci USA. 98(24):13763-13768 (2001).
[cited by applicant]
Eyer, Klaus. et al. A microchamber array for single cell isolation and analysis of intracellular biomolecules. Lab on a Chip 12(4):765-772 (2012).
[cited by applicant]
Eyer, Klaus. et al. Implementing enzyme-linked immunosorbent assays on a microfluidic chip to quantify intracellular molecules in single cells. Analytical Chemistry 85(6):3280-3287 (2013).
[cited by applicant]
Fairbanks, Benjamin D. et al. A Versatile Synthetic Extracellular Matrix Mimic via Thiol-Norbornene Photopolymerization. Advanced Materials 21(48):5005-5010 (2009).
[cited by applicant]
Fairbanks, Benjamin D. et al. Photodegradable, Photoadaptable Hydrogels via Radical-Mediated Disulfide Fragmentation Reaction. Macromolecules 44(8):2444-2450 (2011).
[cited by applicant]
Fattahi, et al., Photodegradable hydrogels for rapid screening, isolationm and genetic characterization of bacteria with rare phenotypes. Biomacromolecules, ACS, Jun. 19, 2020; 12 Pages.
[cited by applicant]
Fattahi, Niloufar. Hydrogel interfaces for applications in microbial biotechnology. 2021. 172 Pages.
[cited by applicant]
Fischbach, Michael A. et al. Cell-based Therapeutics: the Next Pillar of Medicine. Science Translational Medicine 5(179):179ps7, 1-6 (2013).
[cited by applicant]
Fu, Xiaonan et al., Continuous polony gels for tissue mapping with high resolution and RNA capture efficiency. bioRxiv (2021.03.17.435795).
[cited by applicant]
Gao, Shipeng et al. Oriented immobilization of antibodies onto sensing platforms-A critical review. Analytica chimica acta 1189:338907, 1-24 (2022).
[cited by applicant]
Garagorri, Nerea et al. Keratocyte behavior in three-dimensional photopolymerizable poly(ethylene glycol) hydrogels. Acta Biomaterialia 4(5):1139-1147 (2008).
[cited by applicant]
Gauvin et al, “Microfabrication of complex porous tissue engineering scaffolds using 3D projection stereolithography,” Biomaterials, 33(15): 3824-3834 (2012).
[cited by applicant]
Geckil et al., “Engineering hydrogels as extracellular matrix mimics,” Nanomedicine (Lond.) 5(3):469-484 (2010).
[cited by applicant]
Goldring, Chris E P. et al. Assessing the safety of stem cell therapeutics. Cell Stem Cell 8(6):618-628 (2011).
[cited by applicant]
Greenberg, Marc M, and John L. Gilmore. Cleavage of Oligonucleotides from Solid-Phase Supports Using o-Nitrobenzyl Photochemistry. 59(4):746-753 (1994).
[cited by applicant]
Griffin et al, “Photodegradable macromers and hydrogels for live cell encapsulation and release,” J. Amer. Chem. Soc., 134: 13103-13107 (2012).
[cited by applicant]
Gunderson, Kevin L. et al. Decoding randomly ordered DNA arrays. Genome Research 14(5):870-877 (2004).
[cited by applicant]
Haeberle, Stefan, and Roland Zengerle. Microfluidic platforms for lab-on-a-chip applications. Lab on a chip 7(9):1094-1110 (2007).
[cited by applicant]
Hahn et al., “Photolithographic patterning of polyethylene glycol hydrogels,” Biomaterials, 27: 2519-2524 (2006).
[cited by applicant]
Hammoudi et al, “Long-term spatially defined coculture within three-dimensional photopatterned hydrogels,” Tissue Engineering, 16(6): 1621-1628 (2010).
[cited by applicant]
Han et al, “Fabrication of three-dimensional scaffolds for heterogeneous tissue engineering,” Biomed. Microdevices, 12: 721-725 (2010).
[cited by applicant]
Hashimshony, Tamar et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biology 17:77, 1-7 (2016).
[cited by applicant]
Heo et al, “A microfluidic bioreactor based on hydrogel-entrapped
[cited by applicant]
Holmes, Christopher P. Model Studies for New o-Nitrobenzyl Photolabile Linkers: Substituent Effects on the Rates of Photochemical Cleavage. The Journal of Organic Chemistry 62(8):2370- 2380 (1997).
[cited by applicant]
Hong et al, “Cell microarray technologies for high-throughput cell-based sensors,” Sensors, 17:1293 (2017).
[cited by applicant]
Hou, Ping et al. Photo-cross-linked biodegradable hydrogels based on n-arm-poly(ethylene glycol), poly(ε-caprolactone) and/or methacrylic acid for controlled drug release. Journal of biomaterials applications 32(4):511-…
[cited by applicant]
Hou, Young et al. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. Gigascience 4:37, 1-16 (2015).
[cited by applicant]
Huang et al., “Light-addressed electrodeposition of enzyme-entrapped chitosan membranes for multiplexed enzyme-based bioassays using a digital micromirror device,” Sensors, 13: 10711-10724 (2013).
[cited by applicant]
Huang, Shih-Hao et al. Light-addressable Electrodeposition of Cell-encapsulated Alginate Hydrogels for a Cellular Microarray Using a Digital Micromirror Device. Biomicrofluidics 5(3):34109-1-34109-10 (2011).
[cited by applicant]
Ifkovits et al., “Review: Photopolymerizable and degradable biomaterials for tissue engineering applications,” Tissue Engineering, 13(10): 2369-2385 (2007).
[cited by applicant]
Jen, Chun-Ping et al. Single-cell chemical lysis on microfluidic chips with arrays of microwells. Sensors 12(1):347-358 (2012). Published Online Dec. 30, 2011.
[cited by applicant]
Jung, Sukwon et al. Controlled network structures of chitosan-poly(ethylene glycol) hydrogel microspheres and their impact on protein conjugation. Biochemical Engineering Journal 135:123-132 (2018).
[cited by applicant]
Kabb, Christopher P. et al. Photoreversible Covalent Hydrogels for Soft-Matter Additive Manufacturing. ACS Applied Materials and Interfaces 10(19):16793-16801(2018).
[cited by applicant]
Kahl, Jeffrey D, and Marc M. Greenberg. Solution-Phase Bioconjugate Synthesis Using Protected Oligonucleotides Containing 3′-Alkyl Carboxylic Acids. The Journal of Organic Chemistry 64(2):507-510 (1999).
[cited by applicant]
Kahl, Jeffrey D. et al. High-Yielding Method for On-col. Derivatization of Protected Oligodeoxy-nucleotides and Its Application to the Convergent Synthesis of 5′,3′-Bis-conjugates. Journal of Organic Chemistry 63(15):48…
[cited by applicant]
Kang, Joo H. et al, Analysis of pressure-driven air bubble elimination in a microfluidic device. Lab on a Chip. 8:176-178 (2008).
[cited by applicant]
Kharkar, Prathamesh M. et al. Design of Thiol- and Light-sensitive Degradable Hydrogels using Michael-type Addition Reactions. Polymer Chemistry. 6(31):5565-5574 (2015).
[cited by applicant]
Kharkar, Prathamesh M et al. Designing degradable hydrogels for orthogonal control of cell microenvironments. Chem Soc Rev 42(17):7335-7372 (2013).
[cited by applicant]
Kikuchi et al., “Arraying heterotypic single cells on photoactivatable cell-culturing substrates,” Langmuir, 24: 13084-13095 (2008).
[cited by applicant]
Kim, Sung Ah. et al. An Efficient and Reliable DNA Extraction Method for Preimplantation Genetic Diagnosis: a Comparison of Allele Drop Out and Amplification Rates Using Different Single Cell Lysis Methods. Fertility an…
[cited by applicant]
Kim, Tae Kyung, and James H Eberwine. Mammalian cell transfection: the present and the future. Analytical and Bioanalytical Chemistry 397(8):3173-3178 (2010).
[cited by applicant]
Kivlehan et al, “Three-dimensional hydrogel structures as optical sensor arrays, or the detection of specific DNA sequences,” Anal. Biochem., 421: 1-8 (2012).
[cited by applicant]
Kloxin et al, “Photodegradable hydrogels for dynamic tuning of physical and chemical properties,” Science, 324(5923): 59-63 (2009).
[cited by applicant]
Koh, “Cell microarrays based on hydrogel microstructures for the application to cell-based biosensor,” Chapter 7, in Biological Microarrays: Methods and Protocols, Methods in Molecular Biology, vol. 671 (2011).
[cited by applicant]
Koh et al, “Fabrication of cell-containing hydrogel microstructures inside fluidic devices that can be used as cell-based biosensors,” Anal. Bioanal. Chem., 385: 1389-1397 (2006).
[cited by applicant]
Koh, Won-Gun. et al. Poly(ethylene glycol) Hydrogel Microstructures Encapsulating Living Cells. Langmuir 18(7):2459-2462 (2002).
[cited by applicant]
Kovac, Joseph. et al. Image-predicated sorting of adherent cells using photopatterned hydrogels. Advanced healthcare materials 2(4):552-556 (2012).
[cited by applicant]
Lee, Jeongwoo. et al. Single-cell multiomics: technologies and data analysis methods. Experimental & Molecular Medicine 52(9):1428-1442 (2020).
[cited by applicant]
Levalley, Paige J. et al. On-demand and tunable dual wavelength release of antibody using light-responsive hydrogels. ACS Appl Bio Mater 3(10):6944-6958 (2020).
[cited by applicant]
Levine, Bruce L. et al. Global Manufacturing of CAR T Cell Therapy. Molecular Therapy. Methods & Clinical Development 4:92-101 (2016).
[cited by applicant]
Lichtenberg, Jessanne Y. et al. Non-specific adsorption reduction methods in biosensing. Sensors 19(11):2488, 1-17 (2019).
[cited by applicant]
Liu et al, “A microfluidic photolithography for controlled encapsulation of single cells inside hydrogel microstructures,” Science China Chemistry, 55(4): 494-501 (2012).
[cited by applicant]
Liu, Yang. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183(6):1665-1681 (2020).
[cited by applicant]
Lu et al, “A digital micro-mirror device-based system for the microfabrication of complex, spatially patterned tissue engineering scaffolds,” J. Biomed. Mater. Research, 77A(2): 396-405 (2006).
[cited by applicant]
Liu et al, “Controlled photopolymerization of hydrogel microstructures inside microchannels for bioassays,” LabChip, 9: 1301-1305 (2009).
[cited by applicant]
Mackay, Ian M. et al. Real-time PCR in virology. Nucleic Acids Research 30(6):1292-1305 (2002).
[cited by applicant]
Mallory, Xian F. et al. Methods for copy No. aberration detection from single-cell DNA-sequencing data. Genome Biology 21:208, 1-22 (2020).
[cited by applicant]
Maruyama, Hisataka. et al. Immobilization of individual cells by local photo-polymerization on a chip. Analyst 130(3):304-310 (2005).
[cited by applicant]
Naiser et al, “A versatile maskless microscope projection photolithography system and its application in light-directed fabrication of DNA microarrays,” Rev. Sci. Instr., 77: 063711 (2006).
[cited by applicant]
Nebbioso, Angela. et al. Time-resolved analysis of DNA-protein interactions in living cells by UV laser pulses. Scientific Reports 7(1):11725, 1-13 (2017).
[cited by applicant]
Negishi et al, “High-throughput manipulation of circulating tumor cells using a multiple single-cell encapsulation system with a digital micromirror device,” Anal. Chem., 90: 9734-9741 (2018).
[cited by applicant]
Neumann, Alexander J. et al. Nondestructive evaluation of a new hydrolytically degradable and photo-clickable PEG hydrogel for cartilage tissue engineering. Acta biomaterialia 39:1-11 (2016).
[cited by applicant]
Nguyen et al., “Photopolymerizable hydrogels for tissue engineering applications,” Biomaterials, 23: 4307-4314 (2002).
[cited by applicant]
Nichol et al, “Cell-laden microengineered gelatin methacrylate hydrogels,” Biomaterials, 31(21):5536-5544 (2010).
[cited by applicant]
Nicodemus et al, “Cell encapsulation in biodegradable hydrogels for tissue engineering applications,” Tissue Engineering, Part B, 14(2): 149-165 (2008).
[cited by applicant]
Oldenhof, et al., Imaging-assisted hydrogel formation for single cell isolation. Sci Rep 10, 6595 (2020). https://doi.org/10.1038/s41598-020-62623-6.
[cited by applicant]
Panda et al., “Stop-flow lithography to generate cell-laden microgel particles,” LabChip, 8(7): 1056-1061 (2008).
[cited by applicant]
Papavasiliou et al., “Three-dimensional patterning of poly(ethylene glycol) hydrogels through surface-initiated photopolymerization,” Tissue Engineering, part C, 14(2): 129-140 (2008).
[cited by applicant]
Paugh, Barbara S. et al. Reference standards for accurate validation and optimization of assays that determine integrated lentiviral vector copy number in transduced cells. Scientific Reports 11:389, 1-9 (2021).
[cited by applicant]
PCT/US2022/011720 International Search Report and Written Opinion dated Jun. 7, 2022.
[cited by applicant]
PCT/US2022/033116 International Search Report and Written Opinion dated Nov. 3, 2022.
[cited by applicant]
PCT/US2023/015806 International Search Report and Written Opinion dated Aug. 4, 2023.
[cited by applicant]
PCT/US2023/015806 Invitation to Pay Additional Fees dated May 22, 2023.
[cited by applicant]
PCT/US2023/017896 International Search Report and Written Opinion dated Jul. 3, 2023.
[cited by applicant]
PCT/US2023/068154 International Search Report and Written Opinion dated Oct. 10, 2023.
[cited by applicant]
PCT/US2023/070428 International Search Report and Written Opinion dated Nov. 6, 2023.
[cited by applicant]
PCT/US2024/059913 International Search Report and Written Opinion dated Apr. 10, 2025.
[cited by applicant]
Picelli, Simone. et al. Tn5 Transposase and Tagmentation Procedures for Massively Scaled Sequencing Projects. Genome Research 24(12):2033-2040 (2014).
[cited by applicant]
Pollock et al., “Highly multiplexed and quantitative cell-surface protein profiling using genetically barcoded antibodies,” Proc. Natl. Acad. Sci., 115(11):2836-2841 (2018).
[cited by applicant]
Pon, Richard T. Solid-Phase Supports for Oligonucleotide Synthesis. Methods in Molecular Biology 20:465-496 (1993).
[cited by applicant]
Porter, Shaina N. et al. Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo. Genome Biology 15:R75, 1-14 (2014).
[cited by applicant]
Quan, Jiayuan. et al. Parallel on-chip Gene Synthesis and Application to Optimization of Protein Expression. Nature biotechnology 29(5):449-452 (2011).
[cited by applicant]
Quan, Li Na. et al. Edge stabilization in reduced-dimensional perovskites. Nature Communications 11(1):170, 1-9 (2020).
[cited by applicant]
Recek, Nina. et al. Protein adsorption on various plasma-treated polyethylene terephthalate substrates. Molecules 18(10): 12441-12463 (2013).
[cited by applicant]
Reimhult, Erik, and Fredrik Hook. Design of surface modifications for nanoscale sensor applications. Sensors 15(1):1635-1675 (2015).
[cited by applicant]
Restifo, Nicholas P. et al. Adoptive Immunotherapy for Cancer: Harnessing the T Cell Response. Nature Reviews. Immunology 12(4):269-281 (2012).
[cited by applicant]
Russell et al., “Mass transfer in rapidly photopolymerized poly(ethylene glycol) hydrogels used for chemical sensing,” Polymer, 42: 4893-4901 (2001).
[cited by applicant]
Saliba, Antoine-Emmanuel et al. Single-cell RNA-seq: advances and future challenges. Nucleic acids research 42(14):8845-8860 (2014).
[cited by applicant]
Schmid, Ingrid et al. Sensitive method for measuring apoptosis and cell surface phenotype in human thymocytes by flow cytometry. Cytometry 15(1):12-20 (1994).
[cited by applicant]
Schmidt, Manfred. et al. High-resolution Insertion-site Analysis by Linear Amplification-mediated PCR (LAM-PCR). Nature Methods 4(12):1051-1057 (2007).
[cited by applicant]
Sekine, Kazuhiko. et al. Panning of Multiple Subsets of Leukocytes on Atibody-decorated Poly(ethylene) Glycol-coated Glass Slides. Journal of Immunological Methods 313(1-2):96-109 (2006).
[cited by applicant]
Serien, Daniela, and Sugioka, Koji. Fabrication of three-dimensional proteinaceous micro- and nano-structures by femtosecond laser cross-linking. Opto-Electronic Advances 1(4):18000801-18000818 (2018).
[cited by applicant]
Serien, Daniela. et al. Femtosecond Laser Direct Write Integration of Multi-Protein Patterns and 3D Microstructures into 3D Glass Microfluidic Devices. Applied Sciences 8(2):147, 1-13 (2018).
[cited by applicant]
Shendure, Jay. et al. Accurate Multiplex Polony Sequencing Of An Evolved Bacterial Genome. Science 309(5741):1728-1732 (2005).
[cited by applicant]
Shifrut, Eric. et al. Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function. Cell 175(7):1958-1971.e1-e15 (2018).
[cited by applicant]
Shih, Han and Lin, Chien-Chi. Cross-linking and degradation of step-growth hydrogels formed by thiol-ene photoclick chemistry. Biomacromolecules 13(7):2003-2012 (2012).
[cited by applicant]
Shin, et al., Photodegradable hydrogels for capture, detection, and release of live cells. Angew Chem Int Ed Engl. Jul. 28, 2014; 53(31): 8221-8224. doi:10.1002/anie.201404323.
[cited by applicant]
Sia, Samuel K, and George M Whitesides. Microfluidic devices fabricated in poly(dimethylsiloxane) for biological studies. Electrophoresis 24(21):3563-3576 (2003).
[cited by applicant]
Singh-Gasson, Sangeet. et al. Maskless Fabrication of Light-directed Oligonucleotide Microarrays Using a Digital Micromirror Array. Nature Biotechnology 17(10):974-978 (1999).
[cited by applicant]
Soman et al, “Digital microfabrication of user-defined 3D microstructures in cell-laden hydrogels,” Biotechnol. Bioeng., 110(11): 3038-3047 (2013).
[cited by applicant]
Southern, Edwin M, and Uwe Maskos. Parallel synthesis and analysis of large Nos. of related chemical compounds: applications to oligonucleotides. Journal of biotechnology 35(2-3):217-227 (1994).
[cited by applicant]
Spencer, Sarah J. et al. Massively Parallel Sequencing of Single Cells by epicPCR Links Functional Genes With Phylogenetic Markers. ISME Journal 10(2):427-436 (2016).
[cited by applicant]
Steinhilber et al., “A microgel construction kit for bioorthogonal encapsulation and pH-controlled release of living cells,” Angew. Chem. Int. Ed., 52: 13538-13543 (2013).
[cited by applicant]
Strategies for Attaching Oligonucleotides to Solid Supports. IDT—Integrated DNA Technologies:1-7 (2014).
[cited by applicant]
Sun, Tao. et al. Image-based single-cell sorting via dual-photopolymerized microwell arrays. Analytical chemistry 86(2):977-981 (2014).
[cited by applicant]
Suri et al, “Solid freeform fabrication of designer scaffolds of hyaluronic acid for nerve tissue engineering,” Biomed. Microdevices, 13: 983-993 (2011).
[cited by applicant]
Suyama et al. “Photobase generators: Recent progress and application trend in polymer systems”, Progress in Polymer Science, 34(2009), 194-209. (Year: 2008).
[cited by applicant]
Tamminen, Manu V, and Marko PJ Virta. Single Gene-based Distinction of Individual Microbial Genomes From a Mixed Population of Microbial Cells. Frontiers in Microbiology 6:195, 1-11 (2015).
[cited by applicant]
Tamura, et al., Optical cell separation from three-dimensional environment in photodegradable hydrogels for pure culture techniques. Scientific Reports, May 7, 2014; 4:4793, DOI: 10.1038/srep04793.
[cited by applicant]
Tanna, Jay G. et al. Critical Testing and Parameters for Consideration When Manufacturing and Evaluating Tumor-associated Antigen-specific T Cells. Cytotherapy 21(3):278-288 (2019).
[cited by applicant]
Thornhill, Alan R. et al. A Comparison of Different Lysis Buffers to Assess Allele Dropout From Single Cells for Preimplantation Genetic Diagnosis. Prenatal Diagnosis 21(6):490-497 (2001).
[cited by applicant]
Tibbit et al, “Hydrogels as extracellular matrix mimics for 3D cell culture,” Biotechnology and Bioengineering, 103(4): 655-663 (2009).
[cited by applicant]
Trilling, Anke K. Antibody orientation on biosensor surfaces: a minireview. Analyst 138(6):1619-1627 (2013).
[cited by applicant]
Tsang et al. Fabrication of 3D hepatic tissues by additive photopatterning of cellular hydrogels. The FASEB Journal 21(3):790-801 (2007).
[cited by applicant]
Tsang. Three-Dimensional Tissue Fabrication, Advanced drug delivery reviews 56(11):1635-1647 (2004).
[cited by applicant]
Tyagarajan et al., “Optimizing CAR-T cell manufacturing processes during pivotal clinical trials,” Molecular Therapy: Methods & Clinical Development, 16: 136-144 (2020).
[cited by applicant]
Underhill et al., “Bioengineering methods for analysis of cells in vitro,” Ann. Rev. Cell Devel. Biol., 28: 385-410 (2012).
[cited by applicant]
Unger, et al. Monolithic microfabricated valves and pumps by multilayer soft lithography. Science. Apr. 7, 2000;288(5463):113-6.
[cited by applicant]
U.S. Appl. No. 17/669,315 Office Action dated Oct. 13, 2023.
[cited by applicant]
U.S. Appl. No. 17/896,742 Office Action dated Sep. 14, 2023.
[cited by applicant]
U.S. Appl. No. 18/219,545 Notice of Allowance dated Jan. 31, 2024.
[cited by applicant]
U.S. Appl. No. 18/219,545 Office Action dated Oct. 18, 2023.
[cited by applicant]
U.S. Appl. No. 17/715,843 Notice of Allowance dated Aug. 31, 2022.
[cited by applicant]
U.S. Appl. No. 17/715,843 Office Action dated Jul. 8, 2022.
[cited by applicant]
U.S. Appl. No. 17/896,742 Office Action dated Mar. 13, 2023.
[cited by applicant]
U.S. Appl. No. 17/896,742 Office Action dated Mar. 22, 2024.
[cited by applicant]
U.S. Appl. No. 17/896,742 Office Action dated Nov. 21, 2022.
[cited by applicant]
U.S. Appl. No. 18/593,787 Non-Final Office Action dated May 7, 2024.
[cited by applicant]
U.S. Appl. No. 18/593,787 Notice of Allowance dated Jul. 11, 2024.
[cited by applicant]
U.S. Appl. No. 18/776,193 Corrected Notice of Allowability dated Apr. 23, 2025.
[cited by applicant]
U.S. Appl. No. 18/776,193 Notice of Allowance dated Jan. 16, 2025.
[cited by applicant]
U.S. Appl. No. 18/776,193 Office Action dated Sep. 16, 2024.
[cited by applicant]
Van Dam, Robert Michael. Solvent-resistant elastomeric microfluidic devices and applications. Doctoral Thesis, California Institute of Technology :1-334 (2005).
[cited by applicant]
Van Der Vlies, et al., On Demand release and retrieval of bacteria from microwell arrays using photodegradable hydrogel membranes. ACS Appl. Bio Mater. 2019, 2, 266-276.
[cited by applicant]
Vaninsberghe, Michael. et al. Highly multiplexed single-cell quantitative PCE. PLoS ONE 13(1):e0191601, 1-18 (2018).
[cited by applicant]
Venkatesan, Hariharan, and Marc M. Greenberg. Improved Utility of Photolabile Solid Phase Synthesis Supports for the Synthesis of Oligonucleotides Containing 3′-Hydroxyl Termini. The Journal of Organic Chemistry 61(2):5…
[cited by applicant]
Verma, Sandeep et al. Modified Oligonucleotides: Synthesis and Strategy for Users. Annual Review of Biochemistry 67(1):99-134 (1998).
[cited by applicant]
Vickovic et al., “Massive and parallel expression profiling using microarrayed single-cell sequencing,” Nature Communications, 7: 13182 (2016).
[cited by applicant]
Vistain, Luke F. and Savas Tay. Single-Cell Proteomics. Trends in Biochemical Sciences. 46(8):661-672 (2021).
[cited by applicant]
Volozonoka, Ludmila et al. Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing. International Journal of Molecular Sciences 23(9):4819, 1-24 (2022).
[cited by applicant]
Wahlgren, Marie, and Thomas Arnebrant. Protein adsorption to solid surfaces. Trends in Biotechnology 9(1):201-208 (1991).
[cited by applicant]
Wang et al., “Broadening cell selection criteria with micropallet arrays of adherent cells,” Cytometry Part A, 71A: 866-874 (2007).
[cited by applicant]
Wang et al, “Micromolded arrays for separation of adherent cells,” LabChip, 10(21): 2917-2924 (2010).
[cited by applicant]
Wang et al, “Micropallet arrays with poly(ethylene glycol) walls,” LabChip, 8(5): 734-740 (2008).
[cited by applicant]
Wang, Xiuyan, and Isabelle Riviere. Clinical Manufacturing of CAR T cells: Foundation of a Promising Therapy. Molecular Therapy Oncolytics 3:16015, 1-7 (2016).
[cited by applicant]
Wang, Xuefeng et al. DNA copy number profiling using single-cell sequencing. Briefings in Bioinformatics 19(5):731-736 (2018).
[cited by applicant]
Wang, Yong and Navin, Nicholas E. Advances and Applications of Single-Cell Sequencing Technologies. molecular cell 58(4):598-609 (2015).
[cited by applicant]
Welch, Joshua D. et al. Selective single cell isolation for genomics using microraft arrays. Nucleic acids research 44(17):8292-8301 (2016).
[cited by applicant]
Williams et al, “Variable cytocompatibility of six cell lines with photoinitiators used for polymerizing hydrogels and cell encapsulation,” Biomaterials, 26: 1211-1218 (2005).
[cited by applicant]
Winther, Jakob R, and Thorpe, Colin. Quantification of thiols and disulfides. Biochimica et Biophysica Acta (BBA) 1840(2):838-846 (2014).
[cited by applicant]
Xu et al, “Development of disposable PDMS micro cell culture analog devices with photopolymerizable hydrogel encapsulating living cells,” Biomed. Microdevices, 14: 409-418 (2012).
[cited by applicant]
Yang et al, “Rapid fabrication of hydrogel microstructures using UV-induced projection printing,” Micromachines, 6:1903-1913 (2015).
[cited by applicant]
Yenkin, Alex L. et al. Mitochondrial Phenotypes Distinguish Pathogenic MFN2 Mutations by Pooled Functional Genomics Screen. bioRxiv preprint: 1-61 (2021).
[cited by applicant]
Yu, Zhilong. et al. Microfluidic Whole Genome Amplification Device for Single Cell Sequencing. Analytical Chemistry 86(19):9386-9390 (2014).
[cited by applicant]
Yuan, Jinzhou, and Peter A Sims. An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq. Scientific Reports 6:33883, 1-10 (2016).
[cited by applicant]
Zguris et al, “A novel single-step fabrication technique to create heterogeneous poly(ethylene glycol) hydrogel microstructures containing multiple phenotypes of mammalian cells, ” Langmuir, 21: 4168-4174 (2005).
[cited by applicant]
Zhang et al, “Rapid fabrication of complex 3D extracellular microenvironments by dynamic optical projection stereolithography,” Adv. Mater., 24(310: 4266-4270 (2012).
[cited by applicant]
Zhang, Lin. et al. Whole Genome Amplification From a Single Cell: Implications for Genetic Analysis. Proceedings of the National Academy of Sciences of the United States of America 89(13):5847-5851 (1992).
[cited by applicant]
Zhu, He. et al. A Miniature Cytometry Platform for Capture and Characterization of T-lymphocytes from Human Blood. Analytica Chimica Acta 608(2):186-196 (2008). Online published Dec. 28, 2007.
[cited by applicant]
Zhu, Y Y. et al. Reverse Transcriptase Template Switching: a SMART Approach for full-length cDNA library Construction. BioTechniques 30(4):892-897 (2001).
[cited by applicant]
Hochgerner, et al. STRT-seq-2i: dual-index 5′ single cell and nucleus RNA-seq on an addressable microwell array. Scientific Reports 7:16327 (2017).
[cited by applicant]
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